Several potential reasons come to mind that I don't have time to address (are you ripping to the portable SSD or elsewhere, do the drive letters ever change, etc.), but to simply reassure yourself that your flacs are all there, why not just do a simple search in Windows File Explorer for any *.flac file on all the drives, portable, and otherwise, that you use and find out 1)if they exist, and 2)WHERE exactly they are. Then at least you can proceed sans nausea.
MusicBee never deletes a file unless you tell it to, and then only to the Recycle Bin.