Not updating since new heads added
I figured out, regardless saving the updates in the text editor, the file was actually unchanged.
Opening file in other editor and saving the changes worked for me.
Like it was already discussed, the files were probably flagged with "assume-unchanged", which basicly tells git that you will not modify the files, so it doesnt need to track changes with them.
However this may be affecting multiple files, and if its a large workspace you might not want to check them all one by one.
After making new changes in the code and saving it, when I tried the git add ./status commands the response was "branch already-up to date".On Windows, git status, uses, among other things, a file's time stamp and changes in the file's size to determine whether or not a file has changed.So since the time stamp wasn't updated, it only had the file size to go by.In the second situation, you actually did edit the right file, but your command line git won't recognize the change because you're not in the correct directory on the command line. My story is bit funny but I thought it can happen with someone who might be having a similar scenario so sharing it here.
Actually on my machine, I had two separate git repositories .
It does NOT make symlinks, but does a DEEP copy of the source to the dest I experienced same behavior as OP on a MINGW64 terminal from Git Bash for Windows (version 2.16.2) to realize that my 'edited' changes actually were in the original directory, and my git bash commands were from within a deep copy that had remained unchanged.