Weird black patch appear in Photoshop files

Hi, I'm working on a comic, and only recently I've discovered black patch appear in some of the files. It does not present when I open the file in Photoshop, but once saved in JPEG the black patch appears. Attached are the original file of what it should look like and the black patch once the file is saved in JPEG. When I discovered this problem, another symptom is that whenever I draw into the area of dark patches my brushes create weird artefacts that comes and goes; see the linework file, when I draw on it, it creates these black boundaries that just makes it very difficult to draw on. Does anyone have the same problem? and how do you fix it? 

I've just updated my Mac OS(Catalina V 10.15.5) and Photoshop CC(21.1.3) to the latest versions, but that doesn't seem to fix the problem. I've also deleted the preferences and that didn't help either. The file is in a long scrolling format dimension 1600 x 13351 px, could that be a problem? If so, is there a way to work around it?

If anyone has a solution, it'd be a huge help. I'm aiming to export the comic very soon.

Thank you.