My first question is what information does avid show for the dnx version of the media. Clip name, reel name/id and timecode.
Then concentrate on 1 clip. Find the first clip in the show on the USB drive. Link to that clip. Look at it’s related metadata, and decide what is missing, or different that is stopping Avid from relinking.
Reel information incorrectly logged during the transcode is a big issue, as is timecode framerate conversion.
If the timecodes don’t match, you are in trouble, and may have to start creating a second timecode column, and entering some manual information to help the relink process.
If it is a naming reel information issue, you may be able to duplicate the correct information to a different column, and relink using that column.
If you can’t select that sequence, and that 1 clip, and do a relink based on selected clips on open bins, you must figure out what is different. There isn’t much need to fight with 1000 clips over 12 drives, if you can’t do a single clip.
Start small and work your way out.
Glenn