.md Files will not appear in the vault, while appearing inside their respective files

What I’m trying to do

I’ve been adding images to notes of 5e enemies from the SRD zip file and found out there were some enemies missing, which Obsidian would display “Destination folder already exists!” when I tried adding them manually. The search bar showed no results with the same title, but when opening in file explorer the files were, in fact, there, and once I opened said files they would show up in the vault and folder they were supposed to. I have no idea how to fix this without manually opening every file and would appreciate any help regarding this.

(Tl; dr: Obsidian detects notes inside the vault that are not there, but do appear while viewing said vault in file explorer. Once opened they appear normally and I am seeking a practical solution to this besides manually opening A LOT of files)