@capnm - yes, I think there is an unavoidable limitation in the way calibre's device book matching works that if people "mess about" with the books in terms of metadata then all bets are off when it comes to orphaning.
I would not expect there to be any issue if someone just edits a format and re-sends it, provided the title/author is unchanged. However by creating copies of records, then merging the wrong way etc I am not surprised you have orphaning issues.
Personally I would just rely on an external backup for a format if I was concerned I would screw it up with my editing/conversion rather than creating more book records (and hence another calibre unique id which would cause the old id to fall off any lists if merged into that new record). Or use calibre's own conversion backup stuff. I think creating new book entries and merging between etc is making life a bit harder for yourself but if it is a workflow you feel comfortable with then I can't argue with it
It is also another reason why the only books I send to my Kindle come from my "cleaned up library" where my metadata is 100% sorted and books are reformatted. On rare occasions when I read the book I find additional typos or whatever within the text, but unless I plan on offering the book to someone else I am rarely bothered to fix them as I am unlikely to re-read myself (with a TBR backlog already many years long!). However when a rare occasion arises, a simple edit of the book in Sigil of the ePub, reconverting the MOBI and just sending it to the device again has caused no issues whatsoever.