Hi!
I been having this problem for a long time, but never posted about it because I believe it might be very specific to the way I'm using musicbee.
The problem is that previously played files outside my library folder get re-added to the library, but only when I open my instance of MusicBee in a different machine.
Right now I'm using MusicBee as my main player, as a portable application that is synchronized between two Windows machines using MegaSync. I have my music folders in sync as well using MegaSync and using the same folder structure and drive letters. I'm using MusicBee v3.5.8698 P.
I have a few songs and samples in my "Downloads" folder that at some point I played with MusicBee that started to appear in my Inbox even though they are located ouside my Library folder. If I deleted them from my inbox, and then restarted MusicBee on the same machine, they woouldn't pop up again. But once I went to my other machine, they would reappear in my inbox.
Now, I accidentally added everything in my inbox (thinking they were gone) to my library and now they re-appear in my library, again, everytime I switch machines, without even going into my inbox. Everything else in my music folder does go through my Inbox first.