Upgrade to Thunderbird 31.3.0 and lost all previous email settings

The Thunderbird upgrade installer doesn't touch the data at all in the process, so the upgrade itself is likely unrelated... though it can point to a larger issue with a drive (as seen in point 3). Generally, when you get the prompt of it being a fresh install, 1 of 3 things is happening:

1. You're accidentally launching it in local mode. This occurs by running thunderbird.exe directly, which will happen if you set it as your default mail client and run it from another app. Be sure to run ThunderbirdPortable.exe directly.

2. It was installed to a new location. This occurs sometimes when people manually upgrade and accidentally install to a new location, often by selecting the wrong path to install to. Sometimes people select something like X:\PortableApps\ThunderbirdPortable when they browse to select a location, resulting in a path of X:\PortableApps\ThunderbirdPortable\ThunderbirdPortable. If you're upgrading with the PA.c Platform, this can't happen.

3. prefs.js has been corrupted. This occurs occasionally with both local and portable Thunderbird. It is more common with the portable version in situations when run on an external drive as if the drive disconnects while Thunderbird is saving a settings change, that file is now corrupt. prefs.js is a file which stores all the details on your configuration and all your mail accounts. When this file is corrupted or lost, Thunderbird starts in bare/new mode and prompts for a new mail account. Note that none of your existing locally stored email is affected. If this occurs, simply restore from a recent backup of the prefs.js file to regain access to everything. It's located in ThunderbirdPortable\Data\profile

Note that if #3 is the case, you should definitely check the drive for errors and backup more frequently as it could be indicative of a failing drive. A corruption of a file after upgrading the app (lots of writes) lends more credence to a failing drive.