I wrote this long reply and then though lets go back to basics. and start again. Ensure Thunderbird is not running Windows key + R Type %appdata% Delete the Thunderbird folder you see in File Manager.

This will delete everything in the new Thunderbird installation. It will be back to a "just installed" start.

Run Thunderbird and tell it you will configure your accounts later from the help menu select troubleshooting information In troubleshooting information click on the show profile button. Close Thunderbird.

Copy the contents of your old profile folder into the one open in the file manager. If you do not get a request to replace files you are probably copying into the wrong place.

check that the prefs.js file is copied as well as your actual mail data. Once the copy is complete Start Thunderbird.

Did it delete mail again? If so check the anti virus/ firewall on the new drive is allowing Thunderbird to actually contact the mail server and get mail. With IMAP accounts failure to contact the server leads to the folders disappearing. Nothing should affect local folders. or the data in them anyway.

I'm not sure what happened, but it wasn't good. I lost Thunderbird 4 months ago and had 2000+ emails on my online mail server. I followed your instructions and Thunderbird downloaded my online emails. That's all it shows that I have. My previous 17 years of emails are gone. I still have my copy of the profile in another folder. Is there any way to merge it, or at least to get Thunderbird to recognize it?

Try pointing the add-on to your old mail folders and see what it can find. https://addons.mozilla.org/en-US/thunderbird/addon/importexporttools/