I don't think anyone has ever come up with a solution to this. I think the reason that Amazon doesn't allow it is because indexing that many books at one time can cause issues with the Kindle. I'd never do it, personally, it can take days to index that many books, and it will kill the battery life until the indexing is complete, making the Kindle practically unusable during that time.
Myself, I keep all of my ebooks in
Calibre, and they are all DRM free. This makes it easy for me to add as many books to my Kindle as I wish. I still only do a few at a time, batching a dozen or so at a time doesn't cause as many problems as moving hundreds of ebooks at once.