As long as you are using MusicBee ver 3.6 there is a simple method to replace a whole album (for example mp3 to flac) that will retain all the original tag data, database data and playlist links:
1. In your MB library, find the album that you want to replace and select all the tracks.
2. Right-click > Send To > Folder (Replace) > Replace The Selected Files...
3. In the browser window that opens, navigate to the new files (i.e. the flac versions) and select all.
VERY IMPORTANT: YOU MUST ENSURE THAT YOU HAVE THE SAME NUMBER OF ORIGINAL AND NEW FILES AND THAT THE TRACKS ARE IN THE SAME ORDER - there are no safety checks here and it will go wrong if either of these is not correct.
4. Press 'Open', check the confirmation summary displayed and press 'OK'.
That's it: The original files will be replaced with the new ones while retaining the original filename - original files are deleted to the recycle bin.
Obviously you should take the usual back up precautions ahead of trying this.