Hi,
Just want to share that I was experiencing the same error, even without multiple libraries and I fixed it with a simple change - perhaps this is unique to the setup I have. Sharing for community benefit. My setup:
1. While, the PC has the MusicBee Library, my scanned folders (media files repository) are temporarily hosted on LAN on an Android media box, over samba.
2. However, Android or a media player running on it - inbuilt or PowerAmp seems to be updating these files, even though PowerAmp is not configured for this specific folder hosting the repository.
3. All I did is that I made the root folder of the repository "hidden" and since then I am not getting the "The file(s) being edited have been updated outside of Musicbee - you might have to rescan..." notice.
4. The final intended location for the repository is a linux based NAS box, where this sort of touching is unlikely.