So when you transcoded it, you ended up with two AMA clips? Sounds weird.
Note, if the file you AMA linked to is on the drive you use as your Avid media drive, you need to un-check "skip files already existing on target volume" in the Consolidate/Transcode dialog or it won't actually do anything. The AMA clip will still be just sitting there.
Have seen this a few times. I think its just a bug.
I just ignore it.
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