I do use a MF cobol (Visoc), but I'm not sure we use the MF isam indexed files, or at least we use different tools to rebuild (It's repository-driven).
Suggestion: You (should) have a good empty index file. Then copy that over the currently bad indexfile, and perform the rebuild? You might need an extra switch (/b ???) to rebuild the index from data, I don't know. rebuild /? should show available options.
HTH
TonHu