@JSWolf & exaltedwombat - in the OPs original post the number of books to be processed is 35,000, and in another post he/she refers to a friend with a similar issue with a collection of 200,000 books
I read the original problem as being how to upload the 35,000 separate cover images the OP already had into the book folders that were created by adding the 35,000 format files. And in the case of the friend 200,000 images into 200,000 book folders.
Editing thousands of EPUBs with the book editor or uploading thousands of covers via Metadata editor->Change cover->Browse sounds like hard work to me.
As the OP said his solution worked and he didn't have to take out RSI insurance.
BR
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