I haven’t had any success with Bambu Studio accepting files that I have manually zipped by compressing them on a Mac on I think using a ZIP command, but for me it works every time if you use python.
I use the python ZipFile add-in to unzip directly from the 3mf file and back to an updated file. I haven’t made any manual edits to the files - they have all been done with python too.
I generally iterate through every subfile - zipping the ones I am not interested straight back up, and altering the ones I want to change - using for example xml.etree.ElementTree for the XML files
I didn’t do any special compressing of the output zip files - so they are generally much larger than the input files.
If I ever get the hang of GITHUB I will publish a few of my scripts at some point.