Saved passwords / certificates gone after running Migration Assitant

After running and subsequently aborting Migration Assistant on my Mac (migration failed on the other side due to lack of disk space, so it was all aborted), Firefox has lost all certificates and all saved passwords.
Restoring the entire profile directory from a Time Machine backup has had no effect, the data is simply gone.
Is there any way to recover this?

'''''The following doesn't add much to the above, but I'll leave it here anyway.'''''
When you say you ran the Troubleshooter, I'm not sure exactly what you did. Did you use the Safe Mode dialog? Some checkboxes on that dialog do clear settings as noted by their description.
If you do the following, can you find any additional Firefox settings folders (AKA profile folders):
Help > Troubleshooting Information > Show Folder
In the Windows Explorer window, navigate up one level. If you see multiple folders, your settings might be safely stored in a different folder.

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