Look in the MODS folder of your computer Capt Dave J. Harper, and see if it's still there. You may have a mangled SH4 install now also. I'll ask these same questions again though:
1. Which Windows OS do you have, and is it 32-bit or 64-bit?
2. What directory do you have SH4 installed in?
When mention is made of "Windows Protected", it has nothing to do with users allowed on the computer. Here's
Microsoft's explanation of Windows File Protection. They started getting more into the technology back in the Windows 2000 Pro / Windows NT Server days, in an attempt to keep the user from harming their (MS) OS on your computer, and upping their (MS) tech support costs. It has blossomed beyond User Access Control (UAC) into something much more involved.
Suffice to say, you do NOT want to install a game like Silent Hunter 3, 4 or 5 in the Program Files directory, whether it'd be "C:\ Program Files" or "C:\ Program Files (x86)". Or even the Program Data folder nearby. Any attempt to alter files in "Windows Protected Files" territory without use of Windows itself will result in Windows rolling back all changes caught to a previous state, with no user intervention necessary nor wanted. This includes "Mods" and could well be part of your issue.