I have no experience with ClearQAM, but I will just note that if you create an ATSC network you do not have to select any of the pre-defined muxes, Just don't select anything in that dropdown, then try creating each mux manually, selecting the ATSC network with no pre-defined mux, and then for the mux settings use ATSC delivery system, and you can try QAM/AUTO or QAM/256 for the modulation type (if one doesn't work, try the other). The trickiest part will be setting the frequency, which is in Hz (not kHz or mHz). Post #6 in the thread at https://forum.libreelec.tv/thread-1333.html gives the ATSC center frequencies for over-the-air channels but what they would be for ClearQAM channels could vary depending on the cable provider. If I recall correctly, there are maybe two or three popular channel numbering schemes for cable TV and each uses different frequencies. See https://en.wikipedia.org/wiki/North_American_television_frequencies and scroll down to "Cable Television" for a discussion.
I don't remember offhand if the HDHomeRun software will show you the center frequencies of the channels it's able to receive, but if so I would create muxes based on those frequencies. If if doesn't show the center frequency, you may have to add or subtract some fixed amount.
Note if you have already created muxes, you could try editing them and changing the modulation setting to see if that makes any difference in your ability to scan channels.