Quick update:

In Thunderbird email client I found the nstmp folder. But it was missing 2 of the 6 years of emails. I could copy these back to inbox but I am still missing 2 years of emails. Strangly after copying these back, the inbox file was only 2GB while the nstmp file was 2.8 GB: the missing emails are these but not visible.

So I gave up and copied over a backup from a month ago. I am missing inbox's most recent emails but at least I have the history.

Hello

I did not know what is the nstmp folder, found the explanation here:

http://kb.mozillazine.org/Nstmp_folders

so this suggests that upgrading triggered an automatic compact of your mailboxes (seems very strange) and it crashed (low disk space ? the 10000 temp file limit ?)

the temp files would be copies of your emails created during the compact process. Antivirus software sometimes interferes with this process, and cause dataloss.

On your computer, you could copy the temp file to your thunderbird profile under "Mail\Local Folders" to try to get them back.

Do you have any backups?

Thanks Wayne, I never solved this problem, but as explained in my initial note I copied a backup I had made a few weeks earlier: I lost some recent emails but at least had most of the 6 years worth of emails.