@benjaminjay I thought you were asking, and I quote:

What is the best way to fix these ROMs using a Windows PC?

But you fail to mention what kind of ROMs, so I assumed arcade, and the answer is that you need to obtain the right ROM version for the right emulator. They are not interchangeable.

Your second question is quite a bit different than that. I suspect Windows is only going to be able to read the boot partition of an SD card setup with the official image. You will need to load a certain kind of driver to let you read/mount linux drive partitions, or use Linux to read them.

<EDIT> @mitu above has a better suggestion that might work for you. Load the image on the system that is going to run it, then connect to the ROM folders over a network with your windows sysetem to add/remove/replace ROMs.