have the same problem, but on embedded Sybase database ...

Log:

I Server HomeC:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat
initDatasource dbport:2638
Config schema format is upgraded from: 11.0.0.3
Launch FRame
net stop semsrv
initDatasource dbport:2638
C:\Program Files\Symantec\Symantec Endpoint Protection Manager\bin\ODBCUtil.exe localhost null DBA passwordxxxx Embedded
Has valid SAV license
Info>> No SNAC license file in C:\Program Files\Symantec\Symantec Endpoint Protection Manager\tomcat\etc\license
SpmSchemaRemediator>>deleteUnsupportedClientsinSPM>> Started.
SpmSchemaRemediator>>deleteUnsupportedComputers>> UPDATE SEM_COMPUTER SET USN=?,DELETED=? WHERE (COMPUTER_ID NOT IN (SELECT SEM_AGENT.COMPUTER_ID FROM SEM_AGENT WHERE DELETED=?)) AND DELETED=?
SpmSchemaRemediator>>deleteUnsupportedComputers>> Total deleted rows:(0)
SpmSchemaRemediator>>deleteUnsupportedClients>> UPDATE SEM_CLIENT SET USN=?,DELETED=? WHERE (COMPUTER_ID NOT IN (SELECT COMPUTER_ID FROM SEM_COMPUTER WHERE DELETED=?)) AND DELETED=? AND GROUP_IS_OU=0
SpmSchemaRemediator>>deleteUnsupportedClients>> Total deleted rows:(0)
SpmSchemaRemediator>>deleteUnsupportedClientsinSPM>> Finished.
Update Binary File Delete Flag start
Updating Binary_file ID: 'C46B17F633C8E83D4092F7A770AFD73B'
Updating Binary_file ID: 'FE0671B6F7A8416624B79A1977950DAD'
Updating Binary_file ID: '7F6E9B1584765B290D72240E65115226'
Updating Binary_file ID: 'AFA7C0E3AFD2D1C7F81B1731F2F81CD6'
Updating Binary_file ID: 'FAA610C73CE7A60EE842ED7A91587E79'
Updating Binary_file ID: 'FE88A391B8FCFCB48330887F88AF0D18'
Updating Binary_file ID: '513A03AD328FF16C256F7189E32B0012'
Updating Binary_file ID: 'E246FCDD61EB0E8645156857787E8572'
Updating Binary_file ID: 'FBF5928E049ED11FCDCD7C2070D92C2E'
Updating Binary_file ID: '2DD7077E12A7ACE0E2C9E92041778EAA'
Updating Binary_file ID: '3966927C9A59719D257B3EBE29B9E3D4'
Updating Binary_file ID: '8E7F73B32EB9942816FA442DA98152B3'
Updating Binary_file ID: '0BDCAC73BC61A2E7E9FC3A3C71E5B6DA'
Updating Binary_file ID: 'EADB04E91F4EFDD3DC42CC18331BB160'
Updating Binary_file ID: 'C13AF35332BD287061C1EDA2D3587CF6'
Updating Binary_file ID: 'BC455A90C02015F4F39AB09B690A7B28'
Updating Binary_file ID: '84F3B3F71876D9C3B39C8550640EF078'
Updating Binary_file ID: '05084C193EFBBD67FF98E7603D4BCD5A'
Updating Binary_file ID: '5F072B54E9E31C0965353E34764CCC4D'
Updating Binary_file ID: '0586398F6C2FB3D1B278A8BA042A7547'
Updating Binary_file ID: 'DECD90F19924FE2176496829E3B35A5C'
Updating Binary_file ID: 'E577B736DCA6A99BF2B5C2FB22C79287'
Updating Binary_file ID: '1F227899F81DB30F810C89E272AD41E8'
Updating Binary_file ID: 'CA554B8F2D7A6B4D8530B655E77B38B5'
Updating Binary_file ID: '34145A58B517E87F6AEBF44519186195'
Updating Binary_file ID: '2EA2B5980E0C4BE99C012CBC08EF639A'
Updating Binary_file ID: 'AAF6678824BD800350EE8BE3053DAE66'
Updating Binary_file ID: '29C981FC4B2E3AF0AEF44084524E8C4F'
Updating Binary_file ID: '868DE0E7620E239A94077A7DE03EECD4'
Updating Binary_file ID: '4D5156752D7808859D66156BAF57EB21'
Updating Binary_file ID: 'C8C9E1B36F0B93AFE196D7CE3B298874'
Updating Binary_file ID: '00ABF970D4A8E07123491357274E44A3'
Updating Binary_file ID: '4A97AAA449FE29533738731A4FE503F8'
Updating Binary_file ID: 'AB08DB3E6CC0ED749DD23D658F1402A9'
Updating Binary_file ID: 'DE39827A032B0454AE2E6C04E8A5C63E'
Updating Binary_file ID: '978B7521E39DBE159C7B948611FE5C27'
Updating Binary_file ID: '54ABCE10FA3D968E27A424F9B16E250E'
Updating Binary_file ID: '24D54A378D9B1195386CBFF5748DCBBE'
Updating Binary_file ID: '4707AA0B36E77784270610726B74F51C'
Updating Binary_file ID: 'FAC2CB1C8575FA8AC1983C53103560D8'
Updating Binary_file ID: '9B93732179214E4FC9A3009FB74C2828'
Updating Binary_file ID: 'A73C403D63FCE458C85D86EF5EB2B531'
Updating Binary_file ID: 'E91222D65218CA196D66FD1947756EC8'
Updating Binary_file ID: '840FDFB2B3887A6F23A5657A8910F01E'
Updating Binary_file ID: '04F42ED566EE92B3DA03C2CE9829A9E7'
Updating Binary_file ID: '79818B584114DE8ACE45B6F20EBC0A63'
Updating Binary_file ID: 'E9FCEA0F4B2D674B9641F651924A2A92'
Updating Binary_file ID: '43A226BD487E5E5E1E43A6B35F2631FD'
Updating Binary_file ID: '4742A37B63C6EB0463587AFC54F00412'
Updating Binary_file ID: 'F46891EDA30531337A0DA16776F60B06'
Updating Binary_file ID: '7AFD73DE121FF10AD34AB3C21D5940EF'
Updating Binary_file ID: 'B67125F736958D34F8F7B1054EA82E33'
Updating Binary_file ID: 'F062D61DF74CF0161ADF0E440C03C2C7'
Updating Binary_file ID: '9191F8285CA5863D6C4FD45E5160F604'
Updating Binary_file ID: '46AC0561D2237CD60F21343413FBB6ED'
Updating Binary_file ID: '5D24ADE5FC03EC0CB4352B2024A2C348'
Updating Binary_file ID: 'A089238400192ADD5EA365C87E11DDF3'
Updating Binary_file ID: 'C2052841BFC750BF675FDBCECF2B65B5'
Updating Binary_file ID: 'C5AC7876842FA4B0C57F6B91D7B7F200'
Updating Binary_file ID: 'F171D3B10F6041DCA978D4C727AE0137'
Updating Binary_file ID: '91ECE41EA51F4B117DE823A37D8080B0'
Removed Refs for : Binary Id : 541CAA6BA2B0EB76767EB90911307406
Removed Refs for : Binary Id : 25480E9D2F5FA568B7A4E03201E43649
Updating Binary_file ID: '18D4D9C15A397EB1B597BBA25BA063B3'
Updating Binary_file ID: 'EC735B60DEC03B17A69C87A071DFDB34'
Updating Binary_file ID: '087458CE61F82DE9FA6EFC18C0DBB552'
Updating Binary_file ID: '4CAEA3A0FEBB425C980E6ED7690EC6E0'
Updating Binary_file ID: '46A0A04EE9CEE2CFEFDEFD0A8FD26AC4'
Updating Binary_file ID: '33F1979B2E1A59A5D233A25068257ADA'
Updating Binary_file ID: '0D490A657C07CD05928AB44D477D1B5C'
Updating Binary_file ID: '2F0C2B18F8E5E334E6569BB73B82FEC1'
Updating Binary_file ID: '46F97ABCA0C77BB088F500E19C0918F3'
Updating Binary_file ID: '2CE598D91AFB85F5C7C506C1C520D79D'
Updating Binary_file ID: '3A661EC43F5A97AF616EC41D56E10FC0'
Updating Binary_file ID: 'BBE8FDF2ED3FBB8086CED312DAAF4807'
Updating Binary_file ID: '600F696E97BABEFF42080FE4B770D3D0'
Updating Binary_file ID: 'E838069A03026CF90DD6A6B83D99E407'
Updating Binary_file ID: '8A3B638E00B469B17276687597E9B6C0'
Updating Binary_file ID: '8D2B01424B36EA2ED15BC2A0538102F3'
Updating Binary_file ID: '9B1683177573126F61281D3F11C0C1FB'
Updating Binary_file ID: '10CE6F5B1072758B6B82D130EE28F634'
Updating Binary_file ID: '56FD5333EC850A84365BFDB99B3367A0'
Updating Binary_file ID: '89046E17F9D9ED636EA5026A978E2DE4'
Updating Binary_file ID: '9F9219514482C1150FBDE79E44ECEC96'
Updating Binary_file ID: '936994F9D2DE650C6DB509E0B08B59B3'
Updating Binary_file ID: '002C3C03DB6777CB17E00891D27FFAAB'
Updating Binary_file ID: '293DC420CBC08C2440D5F4453F835303'
Updating Binary_file ID: 'C47DA1F72825471FB9EC2E1E8DC4925B'
Updating Binary_file ID: '3E128D82970BE66AF2A9A14BAEE52214'
Updating Binary_file ID: '7382F9826E2FB0D52CBF5BF0E08C191D'
Updating Binary_file ID: '4F609D96BDE9A25E84297EF1E5FE95DB'
Updating Binary_file ID: 'DBC5140517AF0F695C472DC8C6D43714'
Updating Binary_file ID: '8CA4D9BF6BEFCE66AC6C3EF144B2AC8C'
UPDATE SQL : UPDATE BINARY_FILE SET DELETED=0 WHERE ID IN ('C46B17F633C8E83D4092F7A770AFD73B', 'FE0671B6F7A8416624B79A1977950DAD', '7F6E9B1584765B290D72240E65115226', 'AFA7C0E3AFD2D1C7F81B1731F2F81CD6', 'FAA610C73CE7A60EE842ED7A91587E79', 'FE88A391B8FCFCB48330887F88AF0D18', '513A03AD328FF16C256F7189E32B0012', 'E246FCDD61EB0E8645156857787E8572', 'FBF5928E049ED11FCDCD7C2070D92C2E', '2DD7077E12A7ACE0E2C9E92041778EAA', '3966927C9A59719D257B3EBE29B9E3D4', '8E7F73B32EB9942816FA442DA98152B3', '0BDCAC73BC61A2E7E9FC3A3C71E5B6DA', 'EADB04E91F4EFDD3DC42CC18331BB160', 'C13AF35332BD287061C1EDA2D3587CF6', 'BC455A90C02015F4F39AB09B690A7B28', '84F3B3F71876D9C3B39C8550640EF078', '05084C193EFBBD67FF98E7603D4BCD5A', '5F072B54E9E31C0965353E34764CCC4D', '0586398F6C2FB3D1B278A8BA042A7547', 'DECD90F19924FE2176496829E3B35A5C', 'E577B736DCA6A99BF2B5C2FB22C79287', '1F227899F81DB30F810C89E272AD41E8', 'CA554B8F2D7A6B4D8530B655E77B38B5', '34145A58B517E87F6AEBF44519186195', '2EA2B5980E0C4BE99C012CBC08EF639A', 'AAF6678824BD800350EE8BE3053DAE66', '29C981FC4B2E3AF0AEF44084524E8C4F', '868DE0E7620E239A94077A7DE03EECD4', '4D5156752D7808859D66156BAF57EB21', 'C8C9E1B36F0B93AFE196D7CE3B298874', '00ABF970D4A8E07123491357274E44A3', '4A97AAA449FE29533738731A4FE503F8', 'AB08DB3E6CC0ED749DD23D658F1402A9', 'DE39827A032B0454AE2E6C04E8A5C63E', '978B7521E39DBE159C7B948611FE5C27', '54ABCE10FA3D968E27A424F9B16E250E', '24D54A378D9B1195386CBFF5748DCBBE', '4707AA0B36E77784270610726B74F51C', 'FAC2CB1C8575FA8AC1983C53103560D8', '9B93732179214E4FC9A3009FB74C2828', 'A73C403D63FCE458C85D86EF5EB2B531', 'E91222D65218CA196D66FD1947756EC8', '840FDFB2B3887A6F23A5657A8910F01E', '04F42ED566EE92B3DA03C2CE9829A9E7', '79818B584114DE8ACE45B6F20EBC0A63', 'E9FCEA0F4B2D674B9641F651924A2A92', '43A226BD487E5E5E1E43A6B35F2631FD', '4742A37B63C6EB0463587AFC54F00412', 'F46891EDA30531337A0DA16776F60B06', '7AFD73DE121FF10AD34AB3C21D5940EF', 'B67125F736958D34F8F7B1054EA82E33', 'F062D61DF74CF0161ADF0E440C03C2C7', '9191F8285CA5863D6C4FD45E5160F604', '46AC0561D2237CD60F21343413FBB6ED', '5D24ADE5FC03EC0CB4352B2024A2C348', 'A089238400192ADD5EA365C87E11DDF3', 'C2052841BFC750BF675FDBCECF2B65B5', 'C5AC7876842FA4B0C57F6B91D7B7F200', 'F171D3B10F6041DCA978D4C727AE0137', '91ECE41EA51F4B117DE823A37D8080B0', '18D4D9C15A397EB1B597BBA25BA063B3', 'EC735B60DEC03B17A69C87A071DFDB34', '087458CE61F82DE9FA6EFC18C0DBB552', '4CAEA3A0FEBB425C980E6ED7690EC6E0', '46A0A04EE9CEE2CFEFDEFD0A8FD26AC4', '33F1979B2E1A59A5D233A25068257ADA', '0D490A657C07CD05928AB44D477D1B5C', '2F0C2B18F8E5E334E6569BB73B82FEC1', '46F97ABCA0C77BB088F500E19C0918F3', '2CE598D91AFB85F5C7C506C1C520D79D', '3A661EC43F5A97AF616EC41D56E10FC0', 'BBE8FDF2ED3FBB8086CED312DAAF4807', '600F696E97BABEFF42080FE4B770D3D0', 'E838069A03026CF90DD6A6B83D99E407', '8A3B638E00B469B17276687597E9B6C0', '8D2B01424B36EA2ED15BC2A0538102F3', '9B1683177573126F61281D3F11C0C1FB', '10CE6F5B1072758B6B82D130EE28F634', '56FD5333EC850A84365BFDB99B3367A0', '89046E17F9D9ED636EA5026A978E2DE4', '9F9219514482C1150FBDE79E44ECEC96', '936994F9D2DE650C6DB509E0B08B59B3', '002C3C03DB6777CB17E00891D27FFAAB', '293DC420CBC08C2440D5F4453F835303', 'C47DA1F72825471FB9EC2E1E8DC4925B', '3E128D82970BE66AF2A9A14BAEE52214', '7382F9826E2FB0D52CBF5BF0E08C191D', '4F609D96BDE9A25E84297EF1E5FE95DB', 'DBC5140517AF0F695C472DC8C6D43714', '8CA4D9BF6BEFCE66AC6C3EF144B2AC8C') AND DELETED=1
Removed Refs for LUContent :5988D3BED54BA37F23BAE248C4F7FFA5
Removed Refs for LUContent :7AA24BCF1A70D10B4AD6364467F72D13
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> Started.
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> UPDATE BASIC_METADATA SET OWNER = '64B6B7CF0A0A0EC90097177070659207' WHERE ID IN ('0EB6200D0A0A0EC900DBACBFFEE009A5') AND ((OWNER IS NULL) OR (OWNER <> '64B6B7CF0A0A0EC90097177070659207'))
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> UPDATE BASIC_METADATA SET OWNER = '68560C7D0A0A0EC9000A5B0224BC1704' WHERE ID IN ('C42034100A0A0EC901A3BDBC6A51D20E','8CE19FE10A0A0EC9008C7C7F6D2998FD') AND ((OWNER IS NULL) OR (OWNER <> '68560C7D0A0A0EC9000A5B0224BC1704'))
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> UPDATE BASIC_METADATA SET OWNER = '4C3AB26D0A0A0EC90118E146A9CDB06B' WHERE ID IN ('C1649F580A0A0EC90197F7F4612766EC','6D83206B0A0A0EC9001F06836972C1DF') AND ((OWNER IS NULL) OR (OWNER <> '4C3AB26D0A0A0EC90118E146A9CDB06B'))
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> UPDATE BASIC_METADATA SET OWNER = '92608FEA0A0A0EC900B1CF31BE59EBFD' WHERE ID IN ('DAA422410A0A0EC90019F294A6D15138') AND ((OWNER IS NULL) OR (OWNER <> '92608FEA0A0A0EC900B1CF31BE59EBFD'))
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> Total updated rows(1)
SchemaMR2toMR3 upgrade>>setOwnerIdOfAdminDefinedScans>> Finished.
SchemaMR3BetaToMR3 upgrade>>filterUnsupportedEventsInAvPolicies>> Started.
SchemaMR3BetaToMR3 upgrade>>filterUnsupportedEventsInAvPolicies>> Finished.
SoftwarePackageReference: com.sygate.scm.common.configobject.schema.ObjReference@17c4779
SpReference: 8AE82105E1053C53844909AE5B965A69
Found sp: true
SoftwarePackageReference: com.sygate.scm.common.configobject.schema.ObjReference@edf4c8
SpReference: 8AE82105E1053C53844909AE5B965A69
Found sp: true
java.lang.NullPointerException
    at com.sygate.scm.server.upgrade.SchemaMR3BetaToMR3.deleteZeroDeltaFilesIfAny(SchemaMR3BetaToMR3.java:183)
    at com.sygate.scm.server.upgrade.SchemaMR3BetaToMR3.deleteZeroDeltaFiles(SchemaMR3BetaToMR3.java:132)
    at com.sygate.scm.server.upgrade.SchemaMR3BetaToMR3.upgrade(SchemaMR3BetaToMR3.java:108)
    at com.sygate.scm.server.upgrade.SchemaUpgrade.execute(SchemaUpgrade.java:55)
    at com.sygate.scm.server.upgrade.Upgrade.doUpgrade(Upgrade.java:399)
    at com.sygate.scm.server.upgrade.ui.UpgradeTask$ActualTask.<init>(UpgradeTask.java:190)
    at com.sygate.scm.server.upgrade.ui.UpgradeTask$1.construct(UpgradeTask.java:95)
    at com.sygate.scm.server.upgrade.ui.SwingWorker$2.run(SwingWorker.java:121)
    at java.lang.Thread.run(Thread.java:595)
Launching log file ...

Can anybody help ?

This means that you have some files under the "content" folder in SEPM that have a size of zero bytes.  Delete all these files with zero bytes and try the upgrade again.