To tell Git to ignore changes to a file, set the skip worktree option.
git update-index --skip-worktree filename
This will fail loudly when something inevitably go wrong and the file gets changed in an incompatible way, one way or another.
Then you can undo it:
git update-index --no-skip-worktree <file>
git add -p <file>
git update-index --skip-worktree <file>
Found here.