Hello,
I believe you are Migrating from SEP11 RU6MP2 to SEP12.1 RU1, correct?
If yes, then the migration process is correct and there is nothing to worry.
In your case, you are installing SEP 12.1 RU1 i.e; SEP 12.1.1000.157
As per documentation, it is -
"C:\Documents and Settings\All Users\Application Data\Symantec\Symantec Endpoint Protection\CurrentVersion\Data\Definitions\VirusDefs"
i.e;
"C:\Documents and Settings\All Users\Application Data\Symantec\Symantec Endpoint Protection\12.1.1000.157.105\Data\Definitions\VirusDefs"
which is same.
To let you know that starting from SEP 12.1, The Virusdef folder for Symantec Endpoint v12.1 would be under following Locations: -
Win XP - C:\Documents and Settings\All Users\Application Data\Symantec\Symantec Endpoint Protection\CurrentVersion\Data\Definitions\VirusDefs
Win 7 - C:\ProgramData\Symantec\Symantec Endpoint Protection\CurrentVersion\Data\Definitions\VirusDefs
Server 2003 - C:\Documents and Settings\All Users\Application Data\Symantec\Symantec Endpoint Protection\CurrentVersion\Data\Definitions\VirusDefs
Server 2008/R2 - C:\ProgramData\Symantec\Symantec Endpoint Protection\CurrentVersion\Data\Definitions\VirusDefs
Check these Articles:
Drive Space used by Virus Definitions Updates
http://www.symantec.com/docs/TECH141811
Disk Space Management procedures for the Symantec Endpoint Protection Manager
http://www.symantec.com/docs/TECH96214
Hope that helps!!