I think there was one other thing I tried to do which was change the ssl to support another alias but never could get it to accept it fully. Also I tried going into settings where it was server>configure>webmail and clear out the webmail alias and clicked save.
first thing I tried was deleting the templates and switching back the admins one site to the default. I also did immediately check the systemctl status apache2 and nginx which there was a configuration error at the time with the default during one of the changes that I immediately was able to resolve by changing the template and restarting apache2. nginx -t reported fine each time that it was working even right before the crash. the logs were outputting quite a bit of information just that error showed up on every individual log file per domain also but there were a batch of 10 or so logs I should have captured them in my snapshot I made after it went all downhill.
I have it running now with defaults via setting up a new server again and got the htaccess method to work ok for the document root change via apache.
at this point if you need me to look into the bug further let me know in the next few days or I will just scrap the backup of the broken instance.