Munki uses pkgutil to manage what apps need to be installed by creating receipts once an app has been installed.
Occasionally you'll need to force Munki to reinstall an application. Just removing the application from the application folder isn't enough to nudge Munki to reinstall it, you also need to remove the receipt. Once the receipt is removed munki will reinstall the application for you.
The first step is to get the name of the receipt you want to remove. To do this open Terminal.app and enter the following:
This'll produce a list like below:
I want to force Munki to reinstall the fiery printer listed above. To do this I'd type the following:
sudo pkgutil --forget mtdscanonfiery
If this is successful then the Terminal will respond with:
Forgot package 'mtdscanonfiery' on '/'.
Run Managed Software Update again now and it'll reinstall that application.