There are certainly more “foundational” settings that are stored in the show file and not in the scene files. Defining pairs of inputs as “stereo channels” is one such foundational setting. You should consider each band a different “show”, which is really is.
PS – while I haven’t used the CQ system yet, changing stereo pairs in other A&H systems is an audio breaking change. This is likely one of the reasons they have it as a show file setting and not a scene file setting. You really shouldn’t be changing that during a live performance which is what scenes are for.
PSS – This is covered on page 26 of the CQ-18 user guide.
https://www.allen-heath.com/content/uploads/2023/09/CQ_User_Guide_V1_1_0_iss1.pdf