I don’t know the structure of your Flash Drive so I can’t point you in the exact directory. But inside your drive it should be a folder named “.DDJMEMO” usually inside that folder there is an analysis file for each song you have in the drive.
If you have for example an mp3 file name K7 - Come Baby Come (Extended).mp3 you should have an analysis file for that mp3 name K7 - Come Baby Come (Extended).mmp.
Find the corresponding .mmp of the file that is giving you the hard time with the BPM, delete the corresponding analysis file, then export again to the drive with Engine Prime.
It sounds to me that Engine Prime is not overwriting the changes.
Note: Make visible the file extension on the operating system; .wav, .mp3,. doc, .txt, etc.