Rebuild mailbox requires being in Mail, which still doesn't work. Reindex messages was the option I chose. It fired its st started with back up everything. My time machine exceeded its hard drive capacity, so I had to start over with a new time machine on a new hard drive. It took two days to get that process done.
I followed the instructions though I am in V4 because that is where Sierra puts the emails. On the positive side, it does identify which boxes it is rebuilding and I saw the older, most critical email boxes successfully processed (I assume because it moved on to others). Curiously, my apple ID email, which has virtually no other traffic, is huge--took a long time to process. Strange for an unused email address. Immediately after that address, it collapsed as usual telling me only to quit, no other options.
While I am here in the V4 folder, there are a few dozen folders with titles like "A43B62CD-1510-4FAA-AAAB-BF80D9352B70" That particular one is over 17 Gb, over 11 Gb is in the Junk.mbox folder Only two other similar folders are over 1 Gb and none that huge. Opening one of the emails in that folder in text edit, I can see the email address is my apple ID email
I don't know how this email database stores stuff. Is it safe to delete that 11 Gb Junk box? Or does all this have to cross reference?
Also, I have IMAP folder for that address and one other email. I don't recall using IMAP successfully for any of my boxes. All POP. Essentially I am looking for places I can safely delete unnecessary crap to reduce the amount of stuff to be processed and potentially stuff causing problems.