Do you have a save backup prior from the issue happening? Edits from a different program may cause unintended issues that NHSE can't know how to deal with.
I suggest starting over your edits with your backup, NHSE just pulls what it sees from your savedata and if multiple programs are seeing the issue then it's unlikely this is an issue with NHSE.
Do you have a save backup prior from the issue happening? Edits from a different program may cause unintended issues that NHSE can't know how to deal with.