I couldn't autoupdate 2.03 to 2.06, so I replaced my 2.03 NTTE in my mods folder. However, when I loaded NTTE, I was still stuck on 2.03. I had to go to the NTTE installation located in appdata and delete it in order to update properly. Everything seems to be working correctly now, and my progression is fully intact.
The mod is finally EOL and I don't expect any kind of deep inquiry into this or followup patch, but I'd like to leave this comment here in case anyone else is having a similar issue.