Answer by Perry Tew for git rebase: "error: cannot stat 'file': Permission denied"

My encounter with this problem was caused by my editor, Intellij. As part of its internal version controls, it had gone through and locked all hidden git files. (For various reasons, I was not using the git plugin that comes with Intellij...)

So I opened a normal dos window as Administrator, changed to the directory, and executed

attrib -R /S

That removed the lock on the files and everything worked after that and I could sync my changes using the GitHub windows client.