What version of INDI and/or Ekos are you using? StellarMate, AstroBerry, KStars-bleeding stable, nightly?
I am using an ASI6200MM as well for imaging with an ASI120MC-S (USB 3) guide cam and I have problems with imaging as well. It seems that the ASI driver mixes up communication with the ASI6200 and the ASI120. I am using the nightly builds but I have compiled the ASI driver myself using the 1.5.0430 SDK from May 5, 2020, available on the ZWO website.
EDIT: I need to do more tests and collect debug logs to be able to understand what's going on though. Unfortunately I'll need clear skies for that.
Wouter van Reeven
ASI6200MM and 7 slot 2" filter wheel with a SkyWatcher Esprit 80 ED on a SkyWatcher HEQ5-Pro
ASI1600MM-Pro Cooled and 5 slot 1.25" filter wheel with an 8" TS Ritchey-Chrétien on a SkyWatcher EQ6-R
I am using INDI 1.8.0 and was trying to use KStars 3.4.2 but also just python code I wrote to control it. I had my python code working with another CCD and INDI without issue so I figured this would be a easy swap over but that is proving not to be the case. I will try the nightly builds from the ASI Driver SDK and see if that helps, Thanks!