No problem, Harry.
I should have mentioned that all my books are currently AZW3. I originally asked about MOBI as well because I might use that format at some point. The book .mpb1 file in the .Trashes may be from me trying that book out on .mobi before I deleted that version.
It seems .asc is for x-ray and the end of the book while .apnx is for page numbers, but I couldn't find any online info as to what exactly .azw3r or .azw3f are for.
After some experimenting I've found that .azw3r is the notes file. If I add it back to a reloaded book then the notes appear again, whereas that doesn't happen for .azw3f. Adding both files or all the .sdr files back in works too.