Mail folders rejecting emails and emails not showing in Inbox

OK my first problem, just in the passed day or two I started having issues with emails not staying deleted or in folders. Emails reappear, after a short time, in the inbox. I'm not sure how to rememdy this.
Also, still having a problem with emails not staying in the Inbox on Intel Mac Desktop, but showing fine in iPhone mail. What happens here is a new email will drop into Inbox, you can look at it for a few seconds, then it disappears with several others received within hours.
Any help on either issue will be greatly appreciated, this is work email so it's kind of a pain. Thanks!

Eustace, sadly this did not work. It's a full week and I had to keep using Thunderbird to check that I'm not missing any mail. I don't get it, some comes in, some gets left out.
Today I tired Eric Root's reindexing solution and that did not do anything either.
I saw mail bringing in 188 messages and NOTHING new showed up. It did in T-bird because it was all the past week's mail
Thunderbird *****. It doesn't even pay attention to rules I set up in it. I want my Apple mail back!
Can I try to reinstall the mail app from my disks without having to delete the mail app entirely? Will the new files overwrite the old ones and 'freshen' it up (so to speak) and fix this communicaiton issue?

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