(1) You may have misunderstood the issue that let to the discussion: I direct profiled a gained amp and was puzzled why the profile came out with the Kemper gain setting at 0.0 and a super clean tone. I had to increase the gain manually after-the-fact to make the profile sound like the amp. That question has been answered - my error during profiling.
I understand what happened.
What I'm saying is I've never seen this occur, profiling stuff for a relatively long time -- so I'm not sure choosing "clean" is what resulted to the profiling coming out like this. Maybe it can still happen in some rare cases or just hasn't happened to me. Just personally I've always had kemper identify whether the source tone was distorted and still produce a "normal" profile. Whether I've chosen "clean" pre-profiling or not has never made a difference. If there's been distortion in the source tone, and I've chosen "clean", kemper has identified the amp being distorted, and produced a profile with gain control where it should be.
Also reducing the gain on any random distorted kemper profile can make it ultra clean. That's how the gain on kemper works. This isn't an "modelling" emulation of the amp per se, anyway. If what happened here is kemper made a "normal profile" (which of course matches the amp gain), and then for some reason reduced the gain control to 0, that's what would likely happen, I assume. You'd be able to increase gain control on kemper and match the source tone.
What I have seen is a couple of cases where kemper produced a clean tone from a distorted amp -- BUT "clean" being on pre-profiling had no bearing on that. The profile also was not too close to the amp when you'd increase gain on the unit. This is the reason I asked about whether you are certain profile is as close to the amp. At least myself, I'd use similar monitoring, cab, cab emulation, to be certain about how close profile got (and possible to compare direct amp signal with direct profile without cab emulation of course).
In the scenario that the profile matches the amp well enough, as described, I suppose kemper shot an ok profile of the distorted tone... but then for whatever reason gain ended up at 0. It'd be easy to test whether the "clean" setting being on caused this, of course, at least assuming it'd do the same again if on.