The database is present and working, and I was able to recover my keys
using those commands. This indicates Firefox is not reading the database
entry (or it would see the values and work as before). No idea why but
I'll post how to recover the keys  for GAuth Authenticator in case it
helps anyone else:

1) Open your home folder and press CTRL + H to display hidden folders
2) Open folder .http;gauth.apps.gbraad.nl,  inside that open profile folder 
RANDOMCODE.default
3) Copy the file webappstore.sqlite to your Desktop
4) CTRL + ALT + T open a terminal and run: sudo apt-get install sqlite3 && cd 
./Desktop/
5) In terminal: sqlite3 webappsstore.sqlite
6) Open GAuth Authenticator now and click the plus sign to re-add your accounts 
manually. Use the same names & secret keys now displayed in the Terminal.
7) After you have the codes copied & GAuth Authenticator working again, enter 
in terminal to quit sqlite3: .exit

Done, and if anyone else has an easier way to do this please explain as
a comment. This is tested and working for me though probably not the
most elegant workaround.

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https://bugs.launchpad.net/bugs/1260229

Title:
  FF 26 Update resets HTML5 webapps configuration

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