G--I misunderstood. I thought you were going to be managing the retention of the actual mbp and tan files. That is a concern when someone makes a change to the title of a book. Calibre changes the file name, and the mbp file no longer matches, so the notes and highlights are *lost*. They need re-named to the exact file name you used when Calibre sends the book to the device.
After doing metadata changes, I went in via usb and changed the mbp file names myself. I had left them on the Kindle. My understanding is that you are recommending people to clear their Kindle completely, and edit metadata, and re-send all their books via Send to Device. I think this is a little radical. If you are going to recommend this, then you need to tell people to backup those mbp files first (or leave them on the Kindle), and to rename them to match the new filenames on the books after they are sent back via Calibre. And to do it before they open the book, because the Kindle software will immediately create an mbp file with the new name. The re-naming process is complicated by having to delete that one and re-name the one containing the notes. (Or do all this within Calibre.)
I want to make sure I understand what you are going to do. If I do this, and I have 50 screens of highlights in a book, you will put all 50 pages in text format into the Comments box in the Calibre library? I'm not sure I understand the objective, but if people asked for this enhancement they must know what they will do with the data.
When you build a Calibre Catalog, and send it back to the Kindle, the Catalog will contain all 50 pages of highlights as Comments?
Does any of this require allowing Calibre to read the metadata when the Kindle connects to Calibre? I have disabled that as it was taking too long, and I didn't see why you needed to do it. I asked Kovid, but he didn't answer that part of the question.