I have an Plex Pass, an OTA antenna running into an HDHomerun Duo and I use xTeVe. Thanks in advance.

Figured it out finally.... Seems it was the HDHomerun that needed setting up. I went to the Silicone Dust website and downloaded their software for the HDHomerun Duo onto the computer that houses the Plex server. Once that was installed, I ran their software and it identified the HDHomerun and scanned for the OTA channels from there. When that was done I saved it and restarted Plex and suddenly the channels that were missing were there.

Plex was able to allow me to choose and assign my local channels on the HDHomerun DVR and all the other channels stayed the same on the xTeVe DVR. Once I opened Live TV in Plex the locals were in the same guide as the IPTV channels.