@stride-r

Your assessment is absolutely correct. This is a bit tricky for the current version of Zen Cart where mods add code to the file system but Admin Profiles operates from database tables.

It would be possible to perform some reconciliation between the file set and the database to find mods that had been removed, though even then, there's no guarantee that any configuration key groups have been removed.

This will hopefully be much easier to deal with in Zen Cart 2.0 for which a formal plugin system has been announced. I anticipate that this will give Admin Profiles more robust information and a formal installation process into which it may be able to hook.