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There's your problem, as using Undelete and Disable References with the following option
"Set Z position to -30,000" is known to cause this.
You can turn it off if you right click in FNVEdit, select Other, Options, Cleaning, and untick the box.
You'll have to get the uncleaned mod files back before you attempt to clean them again.
Be absolutely sure that the mods really do need cleaning, otherwise just leave them alone.
It should be up to mod authors to clean their own mods, but not all are made with the same level of care.