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No, the procedure of disabling mods is safe for savegames.
You use the most recent save, and after testing, you can simply exit quickly by opening up the console and entering qqq to quit ASAP without having to save. I do this when testing mods.
I'm thinking of the possibility that there may be some munged files somewhere -- textures, meshes, etc -- so try to run chkdsk to check for file integrity.
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