Personally I would remove the USB cable between the prime and TA, run the scan, and see how it behaves and what channels you are "missing" and some could live with that. Without the TA with many areas of spectrum one can view the lineup.json with the ?show=all&tuning parameter
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Rather than disable the DVR, you should probably disable the lower numbered version of the channel that way nothing that uses the modern method tries to use them. Disabling only affects the modern method of tuning not the old WMC way which is dependent on the guide data download (note with some of the "hacks" used to get guide data into WMC, it may check the channels listed by the prime to map)
You are correct that it isn't a spectrum problem (though they possibly could configure the TA to use different frequencies if those SD versions aren't DRM or throw DRM onto the ones specified in the cablecard map). It is a problem that SD has decided to use a device provided lineup and a scan to provide such info (with no manual control) and that cablecards were NEVER MEANT TO BE SCANNED in that way (especially with a TA... years ago I tried a BAN the SCAN initiative but got nowhere) so they are always prone to such errors. I believe I mentioned earlier that I couldn't believe it with how the TA controls things, but there was evidence that to speed up the scan (and a person from SD actually confirmed this back then) that with a TA, they used the cablecard map to more quickly determine drm and subscription status prior to using the TA to actually tune the channels to determine "actual" DRM state when used as intended. The key is the scan must pick up such as being DRM protected and when channels are DRM protected, they can only work with WMC (for recording/live) and things that support DTCP-IP (such as the hdhomerun app on win 10, iOS, and (real) android (note that there are restrictions)).
As it looks, everything is behaving EXACTLY how it should with the exception of the scan and as a result anything that uses that modern method also "breaks". But am surprised that NedS stated "
as when the lower number was tuned by the HDHomeRun app, that should have been seen (though possible he was looking by frequency rather than virtual channel number). So though I am hopeful its something else, I have my doubts since WMC does report such as being protected.