[democrite]

iBooks adds their own to make it simple but that might not be great unless there was syncing and perhaps some future OS X companion or OPDS in Marvin to redownload to a desktop. An order of what seems reliable like the Adept UUID first is an option, and then maybe some id based on file names, paragraph count in a few files, etc. I mostly have commercial, or some from here or made myself so that's what I mostly see. In cases of updates, as long as file order is retained, I can update an ePub in iBooks and keep highlights. Indeed it is hard; I'll continue to think about it.