What is this M3 Lite Pro? The only "Pro"-adapter I can find on M3s website is the M3-Pro-Mini, but you're talking about microSD cards, and AFAIK the only M3-adapter that uses those is M3-perfect-Lite.
Anyways, had similar problems with my M3 Perfect Lite when I updated 28->29, but that was only with saves that were created with 28 still in. Fixed it by copying the saves from the card reflashing the games and replacing the savers with the old ones.