I said a long-ass time ago that I would make a tool for managing the file footers on GBX ROMs and I absolutely never did
Anyway the other day I decided to learn Python and do it, so here it is!
The latest (and only) release as of this writing is v1.0.0-beta.
It can add, edit and remove headers, and also hash ROMs. It's still in a beta state, so I wouldn't call it robust exactly, but I've tested the various operations against some test ROMs and got the expected results. You should definitely verify its output in a hex editor if you're using it for a ROM you plan to release though.
You'll need to install the Python 3 interpreter for your platform to use it. Then, just download the source code zip from the beta release and run gbxtool.py as per the instructions.