Did you try exporting the "fixed" piece only then a simple trim and combine via QuickTime Pro? Sometimes I find that the easiest utility for dirt simple file repair like this. Trim the bad top of the long one. Paste the good top of the new one on just being mindful of the frames where you put the cuts. There are other equally simple edit apps out there, but most of us have QTPro around from the FCP7 days.
Just a thought.
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