I started opening all the files in hope that it will do the same as it did with the map, meaning it will crash when I open it. And well it did.
The problem was with Skeletal Mesh Summer Time. I didn’t thought to check the skeletal meshes, as they were working just fine in a test project using 5.3 what my main project is using, and I tested it just now (in a new 5.3 project), and that mesh is working fine in 5.3 but it crashes the engine in 5.4 with that array line 758 error.
So yeah, I think I will skip the upgrade to 5.4 and wait for 5.5 as I don’t want other stuff to break.