I know its late, As i was waiting i read on a forum to reinstall and start it without mods if that works then subscribe to see what mod if there is one effecting it. So thats what i did before i left out but re subbed them all., I have had no issues or recreations and when i looked in those folders, I couldn't find them files and i put it down to the uninstall. Are there any files i could send that are left over from uninstall that could help with why it happened?
if it happens again i will send them files right over.