That is not a problem with the ebooks it is a problem with using a Kindle.

If you download your book from Amazon to your disk e.g. in Calibre Amazon can't touch it.

I have many amazon books and I read then in pub based readers on my iPhone.

Even on the Kindle I think I am safe as I tend not to use the Amazon link but upload via Calibre so what is on the Kindle does not match what Amazon thinks I have on the Kindle.