If you know the exact file name and path inside the archive you could extract just that file, update it, then UPDATE the archive with it again on the fly.

But that requires that you know EXACTLY the name and path and it has to always be that. Otherwise as Glenn says it becomes much more complicated and you would need to do file cleanup and maybe even a folder of its own for each user/zip file you deal with - or work on them individually which could be a slow process, but safer as well.

Can it be done - YES - is it simple - NO but it can be done.
However it could take a lot of work and time debugging from someone that does understand KiX so you may need to learn KiX some more so that you can debug it or hope that someone here has the time to work with you on debugging it.