You could update your index:
git update-index --assume-unchanged nbproject/project.properties
and make sure it never shows as "updated" in your current repo.
That means it won't ever been pushed, but it is still present in the index.
(and it can be modified at will in your local working tree).
- to revert that state (from git-ready):
git update-index --no-assume-unchanged
- to see all assume unchanged files (from Gabe Kopley's comment)
git ls-files -v | grep '^h '
