AB2012: Apparently they seem to be missing for many people since they recently got changed from "Free when buying another Bethesda game" to simply "Free".
When they went separate several weeks back and some people's libraries were effected by that, I checked even though I could see my game total hadn't changed. They were still there and remained there until a few days ago.
In that time I have constantly been buying new games, and my library was never effected in regard to those two Elder Scrolls games.
So something done by GOG a few days ago, when the Summer Sale finished, changed things.
I've not been manually logged out in all that time, still haven't been.
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I doubt the two games were uninstalled from the OPs PC. It would likely have just been listed title entries in Galaxy were auto removed ... one of the perils of that bloatware program.