With libraw, you can decode a RAW file and then copy its data (or part of it), but then you'd have to save the subframe back as the original format (CR2/NEF..etc) which I don't think it's possible with libraw and even adds more overhead. Currently, after libraw decodes the RAW images, it is subframed if necessary and saved in FITS. libraw frames are always 16bit which might explain why its size is overall larger as some cameras are 10, 12, or 14 bits so it went for 16 to cover all.
I dug a bit deeper and it seems lossless JPEG doesn't offer a handy boundary to do partial image decode like lossy JPEG does as MCU so that point is moot. Canon's CR2 is lossless JPEG encoded internally so the data is smaller compared to raw 14 bit (or 12 with some sensors) data, even though it does have JPEG previews and other metadata embedded.
Ok it's done. It should switch to FITS when doing focus/align/guide and use FITS or Native (depending on your selection in Ekos options) when doing capture.
i tried but now the files saved in capture module are always fits(i changed fits and native in indi control panel but the files saved are always fits).
If you still need any files, I have probably hundreds of raw cr2 files. They are taken with various cameras, various scopes, and various objects. Do you still need any?
Canon Cameras: Canon XSi, Canon 60D
Scopes/Lenses: 12 inch f/4 Newt, 10 inch f/6 Newt, 6 inch f/4 Newt, Rokinon 85 mm Lens, Tamron 18-270 mm Lens, and Canon 10-18 mm Lens