An incremental backup can be used and you can stop that warning message if you edit the backup job so that it inlcudes resetting the archive bit as EV relies on the archive bit to know whether a file has been backed up or not.
You can use the FSAUtility to recall all files. the utility is in the EV install folder. (c:\program files\enterprise vault)
The utilities guide here explains the usage: http://www.symantec.com/business/support/index?page=content&id=TECH140747