We are currently running VirusScan 8.8p1 w' HF793640 in our EPO-managed environment, and we are looking to upgrade to Patch 2. After the upgrade, does each system need to reapply HF793640 or HF793781? If so, will EPO do this automatically?
I don't think so. As the hotfix document states, the hotfix corrects a problem caused by specific dat updates. If you have already updated with the hotfix or successfully updated the dat files past those problematic ones, the problem is solved. No need to apply it again.
Check the Dat version to ensure that it is updating. If it is stuck on an older version, apply the hotfix. Once this is done, upgrade to Patch 2.