Sounds alot as if you have used combined after the model is skinned. Paint skin weight-tool show any list of joints? And don't think any game engines accept that solution either.
Dunno how to solve.
Possibly if you got any older, working version, you could copy/paste the keyframes from broken to working file, and use substitute geometry to update the model. But if thats the case, re-paint weighting it probably easier. Unless someone got any easier trick.