Start over by moving the profile from your old computer to your new.

I would guess that the folders that successfully transferred are within IMAP-connected accounts. Those that have gone missing would then be either POP-connected or Local Folders accounts, which are stored on the old computer and so cannot automatically appear on the new computer.

https://support.mozilla.org/en-US/kb/profiles-where-thunderbird-stores-user-data

I have this problem too. A TB article on this issue stated to copy the TB profile, but the warning was not to copy when either TB is running or that profile is open. Earlier in the article it says to run TB to find the profile. Can someone reconcile this apparent conflict, ie, how to copy when TB is running, yet apparently not to copy when TB running?

Some users panic or glaze over if we try to guide them to burrow into their file system. To get round this, Thunderbird has a function, under Help|Troubleshooting Information, which will open the profile folder in the system file manager.

So:

1. In Thunderbird, go to Help|Troubleshooting Information;
2. Click on Profile folder|Open folder. Your profile opens in Windows Explorer or local equivalent;
3. Close Thunderbird;
4. Do what you need to do using Windows Explorer.