How to restore email including imported mail

Last night I screwed up my new iMac & had to restore entire system from backup. After many hours & help from the Time Machine forum, I was able to restore everything except my emails. I do have all my folders under “On my Mac/ imported” But they are all empty. I’ve been on with Apple support over 1.5 hours (mostly on hold.) Multiple times opening Mail & opening TM & restoring the date/time I wanted & also trying an hour earlier. --No luck.
Strangely,as soon as I open TM (b4 I restore anything) when it says “Today-Now” at the bottom of the screen --My Mail program SEEMS restored to yesterday with all my missing mail in all the correct folders! But as I explained, doing restore, even rebooting does not work. The mail immediately returns to the empty folder version!
It was pointed out to me in TM forum “In Mail use the scroll bar towards the left to scroll all the way to the bottom of your mail boxes. The restored mail should be there. Restored or imported mail doesn't go into your original mail boxes.”
Unbelievable that the Apple support tech didn’t know that! I checked & see a new “Time Machine” White folder containing 14 blue “Recovered Mailbox” 1, 2, 3 etc. All are empty except three which contain slightly different versions of my inbox prior to the data loss. If it was only the inbox I wanted to recover --I’d simply move the 20 + restored messages into my current inbox (if possible) & then delete the restored folders & be done. But, All of my thousands of saved emails from my imported folders are still gone. I’m beginning to suspect that any imported folders under the “On my Mac” section are stored in a different location & must be recovered differently? I wonder how all the other people who restore their entire system restore their email?
Please help!
Thanks,
Steve

This was finally solved by 2nd level Apple tech support. You can read my other post under TM. “Help new Mac user restore entire system”
Summary:
While on hold (forever) I did check the mail folder (Macintosh HD/Users/<user name>/library/Mail) & saw many sub folders were over 100 MB so, I suspected my “missing” mail was actually there. I was on hold 1 3/4 hours waiting for an Apple tech support “Specialist.” He solved it but, it took him 40 minutes. 1st trying a simple open Mail & go into TM & try Restore from the date I wanted. Didn’t work. Then going to the mail folder (Macintosh HD/Users/<user name>/library/Mail) & selecting it & opening TM & again try to restore that folder to the date I wanted. Again, no luck. He then tried to go into Preferences & we did several things (many of which I cannot recall exactly) with com.apple.mail.plist & I think with another file. None worked.
Finally -- He had me open Mail & import from the mail folder (Macintosh HD/Users/<user name>/library/Mail). That Worked! I now had a new folder “Import-2” after Import. (My original Import folder from my initial transfer of mail from my Dell PC via Thunderbird was still there after restore but all the folders were empty.) Now Import-2 had all the folders FULL of my email. I double checked & then deleted my Import folder with all the empty subfolders & then renamed Import-2 to Import. For some reason most of the folders had sort order wrong & some column headings wrong. I fixed all that easily. Strangely, each folder had some emails in yellow & took me quite some time to figure out to simply highlight them all & open color wheel & select black. So, I am back! I’m restored. The Specialist said that the 1st restore attempts SHOULD HAVE worked. He suspected a preferences problem (corrupt file, no way to tell) He said that the mail was there all the time but, just was not showing in the mail program. He had no idea why TM showed it immediately --as if restored -- each & every one of my many TM restore attempts. As soon as I exited TM I was back to empty folders. He said he would do some research & get back to me. He called today & said that The original system restore that DID bring back everything (except my mail) SHOULD have also restored the mail. He said it was an isolated incident & if I ever (shudder!) have to restore entire system once again. It should work properly. If not I will check the mail folder to see if has the mail & if it does, do an import as was the eventual solution this time.
Total time with Apple Tech Support = 3 HOURS, mostly holding.

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