Here are some quick instructions on how to resolve it.

  1. Run a VPS update to the clients from the AEA console. The patch has an update release of 150506-3 which is supposed to be the fix to the false positives.
  2. Do a quick check to see if the clients have updated to this VPS release.
  3. Once the clients have been updated to this VPS release then you can use the AEA to run an Auxiliary task to restore the false positives from the virus chest back to the clients.

Here is a link to the AEA User guide which may help with the above.
http://files.avast.com/files/documentation/enterprise-administration-user-guide.pdf

Cheers
Nick