Unfortunately, it did not remember to leave it as "Native" for some reason. I even changed the camera configuration to be Native but it was still set to FITS in Kstars. In fact, that's exactly what it's set to right now after rebooting to get last night's files off.
In the Ekos configuration panel (the one that pops up when you start INDI) you need to go to the DSLR tab and check the image settings. There RAW should be selected. Then go to the Options tab and click Save. Then in Ekos itself in the CCD tab make sure that Native is selected and then Ekos should remember it. And you don't need to wait for a clear night to test this out
ASI6200 and filter wheel with a SkyWatcher Esprit 80 ED on a SkyWatcher HEQ5-Pro
ASI1600MM-Pro Cooled and filter wheel with an 8" TS Ritchey-Chrétien on a SkyWatcher EQ6-R
Unfortunately, Wouter, this is what I have been doing forever as well, but to no avail. I have saved the configuration with Native selected many times, it just will not keep it. It defaults back to FITS format for me, too. RAW remains checked, but 'Native' will not be remembered.
Along the same lines, the focuser remembers the entered settings for the most part, but when one is not using a filter wheel, it does not remember the preferred exposure time. It always defaults back to 0.5s. It would be great if that could be fixed as well. 0.5s can be awfully short depending on the area of sky one wants to image.
Atlas Pro AZ-EQ, ASI1600MM-Pro, ASI120MM-S, ES102ED, WO-Z61, Nikon D3300, ASI-EFW, ZWO LRGB,Ha,O3,S2 filter set