There are other relinking options within MC that might help you out.
When you select a batch of clips in a bin and try to relink it to a specific sequence, you can select other information inside the bin to use to help find your clips. If you create a sequence of a bins clips- 115 version, and try to relink it to a bin of 36 media, you can select items such as matching masterclip duration or matching master clip end might work. (How many clips in your bin have the exact same duration…down to the frame?) I wouldn’t try to relink 2000 clips at once like this, but bin by bin might work for you.
Doesn’t sound like fun, but you could copy all the original names to a new column, and manually remove the extra letters from the name. They relink according to that bin…like i said, not fun, but feasible.
You are worried about babysitting your new transcodes, but your babysitting time might double or triple that of trying to get the relink to work. Setting your transcodes to go in smaller batches might just save you a lot of time in the end.
Glenn