To be honest, I've never tried it with altered Amazon purchases. I almost always read Amazon's unaltered version on my Kindle and "fix" a backup version that's stored in Calibre. So synchronization always works. I only use this technique for non-amazon content.
I think you need to make sure that your altered amazon ebooks contain anything BUT the real ASIN number in it's metadata to have the best chance of success.
Last edited by DiapDealer; 02-08-2011 at 07:48 PM.