There wont be any issue is you do not upgrade sep client to 12.1
Sepm needs to be upgraded first and not the client
11.0.6 client would be legacy for 12.1 Sepm and can be easily managed by 12.1 sepm not vice versa
sepm 11.0.6 and clients 12.1 no good idea ....
Make sure to copy the db and certificates to another drive before upgrading the sepm
you may also like to copy the policies and add them once the sepm is upgraded to 12.1
Make sure replication is disconnected before upgrade . If replication configured both the sites "Only sepm" needs to be on the same version and reconnect the replication .
Necessary info such as GUP machines configured their host names or Ip address make a note of them .
http://www.symantec.com/business/support/index?page=content&id=DOC4328
there are many good videos and articles on this .
Symantec Endpoint Protection 12.1.1000.157 (RU1) can migrate seamlessly over the following: