I know this is an old post, but I just got the same thing and the same missing files were not being replaced. The problem and the solution is still the same. I was surprised I didn't find much info on this when I looked it up so that is why I am posting this. Someone will need this at some time and no need to make a new post if you can give a solution in an existing one.
They files that are missing are files used in every project so what I did was create a New Empty Project and locate the files missing in the Projects Bar. I then opened the Image Editor by clicking on the missing files and saved them into my project location. I then went back to my project and added them manually.
I tried just finding the file location of every image but couldn't find them all, I can only assume I didn't look hard enough or some of them are being resized.
For the files that are not in every project you can just relocate that files location and add them back in manually. I also had a sound missing.