Mail problem:

The problem as I understand it is that you have a number of Inboxes, but the contents of "All Inboxes" does not correspond to the individual contents of each Inbox. Is that correct?

Try rebuilding each Inbox according to Rebuild mailboxes in Mail on Mac - Apple Support. You can rebuild any Mailbox, or all Mailboxes including each individual Inbox, All Inboxes, Sent, Outbox, Trash, Junk, etc.

The final option is to remove the affected email Account(s), and add them again. If you can’t send or receive email on your Mac - Apple Support describes what to do.

First remove: Log out of or remove email accounts in Mail on Mac - Apple Support

Then add: Add email accounts in Mail on Mac - Apple Support

Be sure to heed the Important note in the first document. It is not clear to me whether the affected email messages are stored in local "On My Mac" Mailboxes or not, so you will want to be completely certain they are safely archived in those local Mailboxes before proceeding with removing the affected Accounts.

As I recall from having used it years ago, Gmail makes it very difficult to actually delete messages. If you can find them on their webmail interface they are almost certainly retrievable should you decide to remove those Gmail accounts and add them again.

Another well-known annoyance is the Goolag's insistence that upon adding their email accounts again, you need to authenticate through a browser and that browser must be Safari. The following Discussion describes it: Can't add google account to Monterey - Apple Community.