As the program and the data are separate then the update deleted nothing. What did happen is another question.

When you started Thunderbird were you asked to create an account like you had never used the program before?

Or are mails simply not listed for some folders or accounts?

Or are folders not appearing where you think they should?

It was like I was starting Thunderbird for the first time. Created the new accounts, although it did pull all the account information over. Just upset that it didn't warn me to back up everything. Had several important emails sitting in my inbox. Went to open Thunderbird and got the message of "Please wait, installing updates". When it opened everything was gone......

If you had to create account all over it is probable it has lost the profile folder. see http://kb.mozillazine.org/Recovering_a_profile_that_suddenly_disappeared