Then your mod stripping must not have been complete enough.
First, unsubscribe to all mods in the Steam Workshop (most mods may be broken by the patch anyway, given, among other things, the changes to religion mechanics).
Then do the following (before launching the game):
1. Go to [Path]\My Documents\My Games\Sid Meier's Civilization VI\Mods and delete all files there.
2. Go one folder up (should be something like [Path]\My Documents\My Games\Sid Meier's Civilization VI) and delete "Mods.sqlite"
3. Go to your Steam Library, right click Civ VI, choose Properties, Local Files and then Verify Integrity.
At this point, the game should no longer recall any mods that you had and any game files that might have been modified by an ill-behaved mod should be restored to their original, unmodified form.
Please report back if that doesn't work.