On the Help/Troubleshooting Information tab, click about:profiles. Is there another profile besides the one in use, and if so, can you select it and 'Launch profile in new browser'?

I've managed to open Thunderbird by going thru C>Program Files and when asked, I chose to skip integration and it looks like everything is back, but I imagine that skipping the integration isn't the proper choice each time I open the program.

Yes, there are 3 profiles showing in About Profiles.

I think that once you have the default profile set correctly, you can set the integration/default email client in Tools/Options/Advanced/General/System Integration, Check Now...

Thanks! Seems to have done the trick!

I have a similar problem after I upgraded Thunderbird 32bit to the 64bit version all my folders disappeared. I was not able to access the account settings nor the options. I uninstalled the 64bit version reinstalled a 32bit version and I had the same problem of folders not showing. I started Thunderbird with the profile manager (-p) and selected the existing profile which is on another partition (not C-drive) but folders still not shown. I downloaded and installed an older 32 bit version (60.9.1), had to select the old profile location again and everything showed up as before. I installed the new 64bit version (68.3.1) and the folders were not showing even after selecting the correct profile and folder again (see screenshot). I realized also after I had used the older Thunderbird 32bit version (60.9.1) an update was made by Thunderbird itself (to version 68.3.1) and then the folders were missing again. When I click on "Get Messages" my email accounts are listed but even when I select any, nothing seems to happen. For now I'll uninstall the 64bit version and the older 32bit version and then I'll try to disable automatic updates. I have several add-ons and I'm wondering if there are any problems with these. I would be glad for some help to solve this.