Is there any ilogic rules in these files that might work on file open or save?
No, after spending hours on it, I realized that I had one file with a weird file name with "#" in it which Inventor didn't like and that one file was causing the Ilogic Copy to fail immaturely.
Look for files with a weird file name such as "#" in it or any other special character which will cause the Ilogic to fail.
In my case I had one file downloaded from a third-party website for a hydraulic cylinder which had that weird name for one of it's part file and I didn't realise first as I had only renamed the assembly but one of it's component file name had "#" in it which was the main culprit. Once I fixed it, it worked.