Well usually when you open the flight sim and it stops to wait for you to click the Update button, that’s usually when you know an update is here. So close the sim at that point, remove the navigraph using the installer, fire up the sim again, click update to download and install the patch. Close the sim again, and then install the navigraph again.
I think it’s pretty hard to miss that it would stop you from going into the sim without clicking the update button at the start.