DavidLock, thanks for the reply.
We did synch the GUIDs on these. And you're right, when you uninstall App B (or A for that matter) the DLLs remain. The problem is that when you re-install App B, it replaces the DLLs. Note that the new and old DLLs have the same exact version -- the vendor never changed the version. The date/time stamp is different but the MSI seems to not check the date/time stamp.
The reason this is important is because our Helpdesk does a lot of uninstalls/re-installs in order to correct problems that occur.
And, yes, if you then verify App A, it does correct it but I'm hoping to be able to avoid that altogether.
We also consider making the DLLs permanent but that does not seem to be a good idea since these DLLs are likely to be upgraded in the future. So, the only other option that we're considering is simply isolating these DLLs.
Thoughts?