@User: There is also a way to do this in magic, but the klayout method is likely to be simpler and more foolproof, so I'd go with that unless you have a specific reason to use magic for doing the update.

I'd still like to know how to do it with magic just to get a better understanding how it works. What I was currently planning to try was to first read the new gds for the subcell with

readonly

and then read the old gds with everything and having the

noduplicates

option set so it wouldn't reaload the cells I already loaded from the new core.