This tool may help you.
You need:
Algorithm employed by this tool:
Copy header from NEW Copy destroyed region from BACKUP Copy rest from NEW Recalculate frame count and put it into header "Destroyed region" is everything in the NEW file up until a long enough piece of common context is found to match between the NEW and the BACKUP file. It works, because FCEU never actually truncates the file. It contains data beyond the movie stream end. This tool just uses the backup file to patch the movie back into good condition.