Whenever you change the software configuration of your systems, you should let your users know and be ready to perform some detective work if seemingly unrelated software suddenly stops working as a result. Make sure you are available to help users with problems after the system is changed in any way.
Before you upgrade your system to new software, check your user community to see which parts of the old software they use, and if they might be inconvenienced by the upgrade. Often users need extra time to switch from one release of an application to a newer version.
If possible, do not strand your users by completely removing the old software. Try to keep both versions on the system until everyone switches to the new version.