I have problems with TB3 also. It seems that the earlier TB was more stable. TB3 seems to be conceived for those with one e-mail account only? If you have many accounts as I do it cannot cope adequately, and you get many problems. It seems to try to make separate folders for each account you have and then gets confused and muddles them, finally deciding that some or all of them do not exist, although as you have discovered they are in reality all there!
I suggest from my experience that your best bet is to back up your e-mail files, delete and then re-install TB. Then import the e-mail files into Thunderbird again. That is what I have to do continuously with TB3 in PCLinux to restore it to run. There seem to be some bugs in TB3?
I have also asked if there are any experts who can give any help with these problems on this forum, but so far there do not seem to be any, or they are too busy to respond.