This really hasn’t anything to do with encryption and possible false positive hit (after the on-line scan) on unencrypted virus pattern files or whether a good AV program cleans up after its self, but one of conflict.

Two AV scanners running at the same time could cause a conflict (some on-line scanners download a virus pattern file that may trigger your resident AV {Panda's does this}). What/which AV deals with a possible infection if on is found, are both trying to repair/delete/move the infected files? I think you can see the possibilities for conflict.

Which AV will deal with the problem of dual detection of a virus (not unencrypted vpf, but real virus) ???

We only give advice, it’s your system and of course you can do what ever you want.