I downloaded your ASTAP stack and will open it up and try it out a little later.
However, a few notes from just reading through your posts and some rudimentary research --
Yes you can put your Bias into both Darks and Dark Flats if you want to set up your calibration that way. Typically I think that is more of a Nikon (D5300 and up) technique, as Canons are better able to utilize real Darks, but the basic calibration formula should work. Though I am a bit confused by your description of a "second run" with the Bias reloaded into Dark Flats. AFAIK if the master flat is already created those ought to be ignored? But if not, the calibration would be incorrect as the flats would be double bias-subtracted. Hmmm.
If you want, take your time with ASTAP and just step through things manually, one-by-one. That'll help to learn it, and every bit of software has a learning curve. Even ST, which you know, is made for beginners.
If you load your dark flats and hit analyze you can see the statistics for each frame. Then, same with the flats. Then there's a button that says replace flats and dark flats with master flat. This happens automatically if you just load everything and hit stack (and that's why your files "disappeared.") Next, same thing with your darks (or whatever you loaded into the darks tab). Finally, lights can be so analyzed, and the stats reviewed to see if you want to cull any bad shots.
Do not worry about 2x G making your images green. They are averaged, not added. This improves the green SNR a bit, however, and that can be taken advantage of in Synth L creation. Ivo takes care of that math, of course, because he's Ivo! Just open or a proper OSC compose will do it. Anyway, the green cast typically found in OSC has more to do with the channel response of the sensor and bayer matrix, where green tends to be the strongest. You can see this if you look up a QE graph for your camera.
I am a bit confused by your equipment here. On page one, the link to your astrobin states you used a Canon 1100Da, so basically a T3, which is an older camera and I would presume fully supported. In fact the linked page states that it is. But, the FITS header in your ASTAP stack claims the camera is a 1500D (i.e. T7), which should also be fully supported (and says so on the list). There really shouldn't be a problem here, so I am a bit confused. If you want, go ahead and link a handful of subs of each type (light, flat, bias - whichever were used) and maybe we can check things out for you.
The FITS header also notes that the debayering pattern used was GBRG.
Is that normal for you? Most cameras I am aware of use RGGB, especially common DSLRs, unless that needs to be switched up due to some kind of file or mirror flipping done in the acquisition stage. So, perhaps it is right, but just something to maybe double-check.
On a quick look at the stack, I think the auto-leveling you did may make it difficult to diagnose many things here (but I don't see any gridding or full color mismatches (usually purple) that are indicative of a bayer pattern error.