Ok, so the data on the smart groups is actually still there too. Before we continue, have you tried restarting your Mac? I ask, because if the databases are where they should be, and the information which DT relies on is also available, then it sounds like DT isn’t using it. Ah, does DT have Full Disk Access? (System Preferences/Security & Privacy/Full Disk Access)
I would make a backup copy of /Users/yourusername/Library/Application Support/DEVONthink 3 before continuing.
When you say the databases are missing, what do you mean? Do you mean the favourites are no longer there, or the list of recently opened databases…? If you open a database from the Finder (by selecting Open from the context menu of the database in Finder), what happens?
Also, if you try to open /Users/yourusername/Library/Application Support/DEVONthink 3/SmartGroups.plist with e.g. TextEdit, does it open (don’t edit it)?
Ok, that’s great - I was just coming to the end of my wisdom
Anyway, don’t you worry - that’s the whole point of helping one another out - different people, different mindsets, different levels of tiredness, whatever - so we all get to have an idea the other didn’t have