Comment 5 for bug 817954

No, I always use the same session and I didn't switch to 2D. It happened right after my every morning update and at that time I didn't do anything else. A look at the update history reveled only few packages which could cause that:
unity-2d:amd64 (3.8.10-0ubuntu2, 3.8.12-0ubuntu1)
unity-2d-places:amd64 (3.8.10-0ubuntu2, 3.8.12-0ubuntu1)
unity-2d-launcher:amd64 (3.8.10-0ubuntu2, 3.8.12-0ubuntu1)

There were no other significant updates which could overwrite unity configuration in dconf. Also please keep in mind that no other settings were lost at that time.

As to ~/.local/share/.converted-launchers -> this one is empty
and ~/.local/share/unity/migration_script.log -> this one doesn't exist on my system.