Apple Mail always needs to "rebuild" Exchange mailbox for new mails
As MS Exchange keeps all of your data on the server there is absolutely no reason why you shouldn't just remove that account. Delete any leftover mailboxes from mail.app and then re-add the Exchange account. I find that often fixes issues between mail.app and Exchange.

As an aside I stopped using mail.app for exchange connectivity (for work) for reasons that there are times when mail.app, Calendar, contacts, reminders, etc. just don't behave as expected when connecting to an Exchange server. Microsoft's (free, last I checked) Outlook client is actually an excellent mail client and I have never had a problem with Outlook on the Mac or on my iPhone.