My Apple Mail is in need of a "refurb", but HOW?

My Apple Mail has become somewhat problematic. I run four mail accounts, including one Gmail. All are IMAP accounts.

Beginning with my upg to BigSur from Mojave the world ain’t anymore as it used to be.
under ‘On my Mac’ I have five BIN (Trash in the US), two JUNK, one DRAFT, one SENT that don’t belong there. When I try to delete one of the BINs, I get an alarming message: " Delete the mailbox “xyz@gmail.com”?** with a warning “Deleting a mailbox permanently removes it and any messages it contains. This action cannot be undone.”

Trying to delete the SENT it tells me " Delete the mailbox “On My Mac”?, Well there ain’t such thing as a mailbox by that name.

The other day all my signatures disappeared, the file that contains them is still there.
I tried to archive all local emails with EagleFiler, but its concept doesn’t do it for me. Too much renaming required.

What is my best plan for a complete overhaul/reset/start from scratch of Apple MAIL?
Suggestions welcome. Thanks.

I upgraded from Mojave directly to Big Sur. Before I did so, I archived all “On Your Mac” emails into EagleFiler. I also emptied my four IMAP accounts prior to the upgrade. Didn’t have any problems except a hang or two during the upgrade.

Before I upgraded to Monterey, I archived all newer email as before. No problems with the email since.

I’m currently testing both EagleFiler and Devon Think Pro as archivers to be used periodically (weekly or so, to archive approx 500 to 1k mails). DTP appears to handle the periodic “deltas” better than EF, which insists on creating new libraries for each archive.

Not sure why renaming would be a problem as both programs preserve the .eml structures of Mail’s filing system…

I’ve become a proponent of getting email out of Mail (app) and into a real database on a routine basis, and certainly before system updates. Too many problems with Mail, but I haven’t found a client I like better.

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@mark4 Thanks for your answer. I understand your approach, but don’t think it would work for me. This is quite likely just down to personal preference. Running two systems, MAIL plus EagleFiler or Devon makes my efforts bigger, not smaller. Again, I appreciate we all have diff ways of thinking. I did give it a try with EagleFiler, but didn’t quite “get it”, conceptually. Having to switch to a separate system to look up related emails is not so much for me. It also needs to be manually updated, yet one more thing to think about.

I’m more looking for a clean get everything out of MAIL, put back in in clean fashion type of thing.

Anybody else with further thoughts? I’d be grateful.

Since all of your accounts are IMAP, have you tried disabling them all in Mail temporarily while you deal with the problematic mailboxes on your Mac?

Here are some results:
The obvious step was of course @chirano 's suggestion. If you are too deep into it, you forget the simple first steps. Thanks.

The real problems were under “On my Mac”. I exported the lot, Apple MAIL’s own export function is sufficient. I went deep into ~/Library/Mail/V8 and deeper and found a good deal of obviously outdated stuff from many years back. For instance a huge mail account from a company I last worked for over 10 years ago which didn’t show up anywhere else on my Mac, and also not in MAIL’s settings, plus various files belonging to MAIL’s database. All backed up, then deleted. All active mail accounts set up afresh, old exported stuff re-imported and MAIL feels a lot snappier.

The V8 store has a few more settings files, almost a completely different set and I don’t mean the ID for each mail account which is a cryptic long number, the latter will be different for newly set up mail accounts.

Obviously MAIL had trouble to migrate in a clean way from the previous Mojave and left a lot of old rubbish behind.

What still gets on my nerves is how Gmail ignores many common IMAP conventions. They really stuff it down one’s throat that only the dreadful labelling is the way to go. You quickly realise IMAP is an afterthought that Google doesn’t like. They even make it difficult to delete old emails. Which part of DELETE do they not understand?

After the entire re-import I found a few DRAFTS for account “A” under TRASH of account “B” and similar things. Thankfully not too many.

Anyway, my MAIL refurb is done now. Like many, I’m still hoping for some better email software, using Outlook will only make it worse.

Wasn’t there a feature to SORT mails in a given mailbox by date, sender, size, asc or desc etc etc. I only see this now in the menus, but wasn’t it in some heading above the list of emails?

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Thank you for this report, I guess. Much of it I didn’t understand, so I might ask questions that a knowledgeable person would think have been answered. I’m especially interested in your experience because just about the time of your first post in this thread, Mail went wonky on my MacBook (but not on my MacBook Air). Also, I have four email accounts: iCloud, Gmail, Gmail, and Exchange.

If I disable the accounts in Mail, can I safely delete the contents of V8 (which, until your post, I didn’t know existed)? Could I simply quit Mail and safely delete the contents?

Mostly I’m interested in the Exchange account, because it is the one that had really strange behavior. (For example, what appeared as one message in the Inbox would display two messages, both apparently in landscape orientation, when I double clicked it. In fact, there were two messages; only one appeared in the Inbox window. Also, an unrelated message was highlighted as if it were part of the same conversation. FWIW, I do not Organize by Conversation, but that was checked after Mail took an inordinately long time to start just before displaying the strange behavior.) On the MBA (which did not have the anomalous behavior), in V8, it appears that there are two folders related to the Exchange account, but one is missing several mailboxes and has some really old mail in it. (I have not look on the MacBook since I read your post.)

I did try to Rebuild the Exchange account on the MacBook. It appeared that Rebuild only affects the currently selected Mailbox rather than the account. Is there a way to Rebuild an account rather than rebuilding each mailbox in the account?

Thanks for any insight, and I apologize for any apparent incoherence.

@Will_M None of your accounts are plain IMAP accounts, but all of mine are. The only similarity is my one Gmail account (but I dislike Gmail and use it as sparingly as I can).
In principle I’m happy to help, but am not sure I can, given the differences.

May I also suggest to start an own thread, this makes it easier for the community to help you.