I installed Netrunner on a separate hard disk with bootloader on that drive.
Windows 7 was installed on a separate ssd.
I can boot into Netrunner fine via F12.
When I try to load windows via the Windows boot loader it fails: “windows loading files” then an error.
Looks like Netrunner hosed my windows boot loader.
Is there any way to fix this within Linux, or do I have to run a Windows repair disk?

The best would be running the Windows repair tool

You are right my friend. I did this today and it worked for me
just insert a repair CD, choose command line,

Thanks - would this work on a UEFI system with GPT disk?