I'm not finding anything that jumps out to me - like are they CBS owned as common thread etc...
There is a clue when some won't transfer. I would normally say you having hard drive issues that is affecting the recordings, even though not all are affected that can easily happen with bad sectors and it depends where the recordings take place on the drive.
But a couple others have said they too have the problem, but I don't see an avalanche of people saying so. That tells me it is most likely and encoding problem that affects locals from some sources.
Take the CBS for instance - you have a problem both OTA and Satellite - I wonder if DISH gets that signal OTA for the Satellite CBS and that's why both are not playing back.
Just throwing out ideas - were any of the channels you are now having a problem with in dispute relatively recently and then restored?
Did they recently do something like some did here - turn on the new ATSC 3.0? Yes they are still broadcasting with the old standard of course nearly no one can receive the 3.0 yet. BUT - when they turned it on here for some of the channels one of those channels went to their own actual frequency separate from it's subchannel actual channel- When they did that, to this day the sub channel (Me TV) at night breaks up a little now and then even with a very strong signal. And now it has the wrong OTA guide for ME TV. It does record and play back however, they all do.
I don't think it is a software issue doesn't seem like anywhere near enough people are complaining about it and it seems to be on both Hopper and a VIP I believe someone reported.