My mom is the primary signer on my car and I'm the co-signer, what will happen if she files bankruptcy and I've been making the payments on time?

Assuming that you continue to make timely payments, upon completion of the obligation, you should suffer no ramifications.  You didn't mention whose name the car is titled in.  If in you mom's, she would have to list the car as an asset and you as a co-debtor in her bankruptcy schedules.  It is doubtful, assuming that the car has equity, that a trustee would take action on the car if you can establish that you have made the payments.  When the debt is retired, I am also assuming that your mother wwould convey the title to you.