I might’ve fixed the bug. So I did finally find a correlation between the images hidden and the images visible. Those that are hidden are those that are directly in the Downloads folder. Whilst those that are visible are in sub-folders of the Downloads folder.
So I checked to see if the Downloads folder was a excluded folder or something. But it was not. And in the included folder, then it would scan the entire phone. So obviously that would include the Downloads folder. And considering it finds files in sub-folders of the Downloads folder, it definitely scans it.
Regardless, what I did was add in the Downloads folder under “Additional included folders”. And suddenly all images came back. But again, this should’ve not been necessary as I’ve always used the same scanning method and all images were properly found before. Either way, it seems to have fixed the problem for now. We’ll see if the bug happens again. But for now it works.
I’ll probably update again in a couple of days if it’s still fixed or not.