I don't have something to help with the current situation, sadly, but this may be helpful in avoiding this issue in the future, assuming that your situation is the same as I recently experienced.
I also had a case where a bunch of images went blank in GMS2 and were missing in the project files, just like you mention.
I'm pretty sure it happened because I lowered the texture page size too small for everything to fit, as everything was assigned to the one texture page (the default one), so that was stupid on my part.
In the end, I had to remake some things, though I had most of my graphics backed up, so I just brought them in again after increasing the texture page size.
Actually, I tried bringing them back in before enlarging the texture size again, because I didn't realize that was the issue, and the problems still occurred, so the issues only stopped after increasing the texture page size, which is why it seems to me that was the issue.
If your case was similar, at least this info may help prevent issues in the future. If not, hopefully it helps someone else.