I never said that it never ever reindexes. I said that during normal operation with correctly formed files which aren't corrupt or malformed then it shouldn't ever reindex unless there is a problem.
If there was such a widespread issue with indexing then I'd expect everybody who has any personal documents on the Kindle to be complaining.
You need to find out what file(s) are actually causing this issue for your Kindle. Load in small batches of files at a time so you can narrow it down.
If you know that every single file is valid then plug it into the charger and leave it indexing. You can plug it into a computer but you can't leave it in USB drive mode. It won't power off if its being charged so the indexing process should be significantly quicker. Once it has completed the index, it shouldn't restart. If it does then there is something wrong.