My deleted mailbox keeps reappearing and my new ones disappear with macOS Mojave

It won't restart in Safe Mode.. I used Recovery mode but nothing changed. Mailbox folders are frozen at about a month ago. Add mailbox, it disappears when I close the app. Deleteted mailboxes reappear, complete with all the mail. Restored V6 folder doesn't fix any problems. Mail app won't update list of mailboxes. It goes back to about a month ago. It's now stuck with the folders. I had. Where is file for the list of mailboxes or whatever determines mailboxes?

Took over an hour to get into Safe mode. Mail app half works. All the mailboxes are in the folder (directory) in V6 directory with all the mail, but the Mail app isn't reading them and creates mail app mailboxes from a month ago without the mail in new or moved folders and all the deleted mailboxes show up. I deleted the envelope files (3 or 5 files, same result. In normal mode it doesn't even find the old mail in the new mailboxes despite mbox file showing content.That's the problem, Mail app is using something wrong to display mailboxes.

What I know so far. The V6 mailbox folder with all the mbox(es) are correct and full. When I open mail I'm getting a listing from months ago without newly added mailboxes, which are empty despite having mail in them before, and with recent deleted mailboxes with all their mail.

There's a disconnect between the mail app and the mail database. Where does mail app get its list of mailboxes? I've deleted the envelope files in maildata before opening app to rebuild the mailboxes, but it just keeps creating the wrong listing, and I can't read the files to know if it's the disconnect.

I've tried Safe Mode and Recovery Mode restoring OS-X. Nothing changed.

I found the missing e-mails and can add and rebuild the mailboxes. The problem is the V6 folder with the .mbox files is correct in the mailboxes and order in the display, and the backupTOC.plist file is correct for the display. The problem is when app is opened it's reading another file with the older mailboxes and order. There are four deleted mailboxes and none of the new ones added. What I need is the list of files in V6/MailData folder to compare list in my Mac. It would help if someone new the file the app reads in user directory to display the mailboxes. Somewhere it's reading a wrong file.

That was a disaster. It reset my mailbox to default style with all the e-mails in inbox, including the 5 accounts, into the one inbox. I quit mail, and restored the folder from clone copy and restarted Mac. It went back to my original problems, deleted folders returned and new folders disappeared. I imported the three new and deleted the old ones. But it's still the problem. It's not reading the right file to display the mailboxes. It's using one months old. but I can't find where it's getting that file.

Do you have a list of the V6/Maildata folder? There was a BackupTOC.plist file in mine with the folder information I suspect the app uses, but the app doesn't read it or look at he list of .mobx files in the folder of mailboxes. I suspect I lost a file or something. Would be nice to have a chart of the folder and files mail app uses. More homework.

I was interested in the MailData folder. Here's mine:

AvailableFeeds

AvailableFeeds-shm

AvailableFeeds-wal

AvailableFeeds.corrupt

BackupTOC.plist

DefaultCounts

Envelope Index

Envelope Index-shm

Envelope Index-wal

Envelope Index..tmp.BjX49F-shm

Envelope Index..tmp.BjX49F-wal

ExternalUpdates.storedata

ExternalUpdates.storedata-shm

ExternalUpdates.storedata-wal

FlagMailboxes.plist

LSMMap2

MessageRules.plist

MessageRules.plist.backup

MessageUidsAlreadyDownloaded3

MessageUidsAlreadyDownloaded3-shm

MessageUidsAlreadyDownloaded3-wal

OpenedAttachmentsV2.plist

RulesActiveState.plist

SearchHistory.plist

Signatures (folder)

SmartMailboxes.plist

SmartMailboxes.plist.backup

SmartMailboxesLocalProperties.plist

SyncAlert

SyncedFilesInfo.plist

SyncedRules.plist

SyncedSmartMailboxes.plist

TOC.plist

UnsyncedRules.plist

VersionedSmartMailboxes.plist

VersionedSmartMailboxes.plist.backup

VIPMailboxes.plist

VIPs.plist

This is where any Table of Contents for Mail folders should be (note BackupTOC.plist).

I'm interested in the list of files in V6/MailData folder to see if I'm missing one. The Mail app has to get the list of mailboxes from somewhere. There's the BackupTOC.plist file with all the folders but the app isn't reading it, but getting it from another file, but what file and where.