When you edit the properties of a song from a single flac album it highlights the entire album. The play count shown in the properties windows will be the total plays from every song off the album, not individual tracks. I had to remove some albums to fix a bug so I wanted to manually add plays back but this is not possible.
I know in foobar2000 you can edit the play count of any track from a single flac album. Would this be possible in MusicBee? Or maybe there is a settings file with all the play counts? In music explorer view it shows the top tracks, so it must be storing that information somewhere.