I’m leaving this message here as it may be useful for future readers (e.g @avatar, who apparently was having a similar issue, as reported here) - at least until the devs implement a permanent fix (if they decide to do so).
With the assistance of the support team, we identified the issue.
Before DT4, I had DT3 installed. When I deleted DT3, its Application Support folder was not deleted. As a result, the following behavior occurred:
- As long as I had at least one favorite in DT4, the Favorites section worked as expected. Adding/removing favorites updated Favorites.plist located in DT4’s Application Support folder: ~/Library/Application Support/DEVONthink/Favorites.plist
- However, when I removed the last favorite, DT4 deleted the Favorites.plist.
- After closing and reopening DT4, the app apparently picked up the DT3 Favorites.plist (still present from the old installation), which in my case contained only one item — the “incriminated” document
— so it kept reappearing as a favorite.
So, for me deleting the DT3 folder in Application Support solved the issue