Thanks for sharing the post!
I am working on a Mac so 7zip is not an option for me. But as Ukdavewood mentioned in the post, Python script with zipfile library works very well.
Here I post my little piece of script in case anyone is interested:
import zipfile
with zipfile.ZipFile('./filename.gcode.3mf', 'a') as z:
z.write('./path/to/your/new.gcode', 'Metadata/plate_1.gcode')