There are scripting functions that allow to search inside a file and modify it.
Here you find some sample scripts: https://www.synalysis.net/scripts.html
These are the steps:
- open the script editor (in the Script menu
- create a script working on files (type "File")
- create a ByteView object using the byteArray parameter
- call findByteSequence() to search for the sequence you mentioned
- call replaceByte() to replace the 0xC0 with 0xFF
- ...
It should also be possible to use a generic script (doesn't operate on the current file) and
- create an empty ByteArray object
- call appendFile("path/to/Borderlands2.exe"
- do the steps above
- call writeToFile("path/to/Borderlands-modified.exe")
Does this help?