Can you switch the thunderbird mail storage to Maildir? I've got Maildir on the server, but locally it stores in a regular Mailbox and builds an index file.
It's possible, I was able to use the method listed under (2) at [1] but it was a few hours of fiddling/restoring backups and even a "102% completed" message before I got it to work. I don't have my notes from the but I believe it involved a second profile at one point so probably pretty similar to method (3) in the end.