Time Machine did not restore hundreds of emails from iCloud email account

All of my various email accounts are POP, except for my iCloud account, which uses IMAP. Recently I accidentally created a rule that deleted all emails older than 60 days old. They may have all been in the Trash, but that would require me to pull them out, and re-add them to the many folders "On my Mac".

So I did a restore of the entire Mail app inside /Library/mail

What a mess Time Machine restore process has made of all my email. I had over 1,000 emails in my main inbox for my iCloud account, and only the emails from today are showing, all the rest are gone.

I have another pop account for my business email. Instead of restoring my entire hierarchy of email folders in Mac Mail, like I assumed a restore process would do, Time Machine dumped over 14,000 emails into the inbox for my business email. Is restoring emails really this bad of a process? Or did something go wrong in my case? What a mess. Not sure what to do at this point, as I can't easily put those 14,000 emails back in their rightful folders "On my Mac"

Help!