How to update packages in Modx (Advanced Installation)?

Hello everyone,
What's the correct way to update packages in Modx 2.2.x (Advanced Installation, Multiple sites with a shared core)?
Using the "Package Manager" will sometimes break the "Package Manager" of other sites which haven't been updated yet.
I assume because the updated package files aren't compatible with the database entires of the previous version.
Any suggestions?
Thank you.
Kind regards, Philipp