Years ago I wrote a post on reordering accounts in Thunderbird and recently found myself needing to do it again. Some of the instructions in the original post are now outdated, so here is the updated version with Windows 10 paths.
In Mozilla Thunderbird each time a new account is added it appears at the bottom of the mail list. I wanted to reorder accounts and move one to the top, but Thunderbird does not have a built in option to reorder accounts. The answer is to edit prefs.js file. On Windows 10 this is located at C:\Users\[usernme]\AppData\Roaming\Thunderbird\Profiles<your profile>pref.js
Look for a line like: user_pref("mail.accountmanager.accounts", "account3,account2,account5,account4,account1");
This is the line you will need to modify to control ordering.
So what does account3 mean and which email account does it match?
In the lines above you will find something like: user_pref("mail.account.account3.identities", "id2");
If the id was 2, search in the prefs.js file for user_pref("mail.identity.id2.useremail". This will give you the matching email address.
One little extra if you wish to make a certain email address at the top. It needs to be made the default. See the line starting with: user_pref("mail.accountmanager.defaultaccount"
Remember, only edit the pref.js file while Thunderbird is closed.
There is also a Thunderbird add on Manually sort folders which should do the same thing.