I have several miultiserver systems and test systems here but I never had it yet that a shell account was not deleted when you delete it in ispconfig.
What you can do is that you change the uids of the ispconfig users that were different in the passwd file on one server so that both files match again and then chown -R the affected website directories manually to this user and group.
We have a bugreport about this issue here:
The issue can happen if you add a shell user manually on one system without adding it on the second server as well. The only solution for that is to use a fixed uid range that ispconfig enforces on both servers, thats a feature which is on our todo list already but it requires some bigger changes.