Possibly a modkit ID conflict (two or more vehicles using the same carcols/carvariations modkit ID number/s) or something wrong in your 'carcols.meta' or 'carvariations.meta' files.
ModKit ID Conflict (diagnosis):
In 'carvariations.meta', set this for both the bikes:
If you get your engine upgrades back after doing that you have a modkit ID conflict.
Unfortunately, due to the way Rockstar did ModkitID's the best approach I know of is to change the numbers until you find one/s that work. Can be a right pain in the hoop if you have lots of add-on vehicles .
See more info & the basics of fixing a modlit ID conflict here.
If you rule out a modkiID conflict, upload the entire 'dlc.rpf' somewhere & I'll download it & take a look