I have the same issue, and it is causing problems when recording as for instance Plex thinks BBC One (1) and BBC One HD (101) are both HD, so Plex no longer always records the HD channel instead of the SD channel. The only way to get it to record BBC One in HD is to now update all my recordings to state only use 101.
Additionally HD Homerun shows only 6 channels as HD channels, which is correct, so am not sure why Plex thinks the other channels are HD.
Seems to be the same issue as this post Program Guide No Longer Showing and Recording HD stations
