Apologies for reviving an old thread but I just had a similar, but much more severe problem.
I decided to change the drive letter of my data drive from 'D:' to 'A:'. I thought nothing more about this for a while, but the next time I started MB, I was told that some tracks were not in the correct place. Looking through the list I saw that all the 'dead' 'D:' links were duplicated in 'A:', so after re-scanning it ought, I thought, to be safe to delete those missing links;
"Sort -> Ctrl+A -> Delete", But they weren't <i>just</i> links...
The result was that 75% of my music files disappeared instantly. I'm a big fan of CCleaner and RemoveEmptyDirectories, so by the time I had traced the problem back to my drive letter change, there was nothing left to recover.
Thankfully the file-tree and 2 to 3 tracks from each album/disc were saved allowing me to rebuild, I presume some were saved by my attempts to 'rescan' the library beforehand, but I'm not sure. On the downside, the next day, thepiratebay was taken down, so it's going to take a while.
To be certain of not making the same mistake again, I recommend a clean uninstall/re-installation of MusicBee, rather than re-scanning the library, just to make sure.