I guess there was something wrong with your Preferences file (it became corrupt for some reason, maybe because of the faulty restart) and it got reset.
There maybe is a Preferences.bak or something similar which is a backup of the corrupt Preferences file. If there is, take a look at it and try to see what is wrong there (it is a JSON file).
All of the other settings were also reset, or only extensions?
Anyway, since every extension has its folder, you can re-install all of the extensions (if all of them were from the extension gallery) by replacing X with the ID of the extension (taken from the folder names in the Extensions folder in the user data directory).
Your data will be saved, because it will use the files from the Local Storage and databases folders, which, as you stated, were not deleted.