While some people have decided to get rid of Flash Player all together, most of us still need to provide the updates to our clients.
The deployment can be easy or not, depending of the update package itself, so I usually test before deploying anything.
When things go wrong, it is sometimes necessary to uninstall flash player and reinstall it.
One side effect of this is that the uninstall will mess with your mms.cfg file: see the note from Flash deployment guide below…
Beginning with Flash Player 11.5, uninstalling the Flash Player resets the AutoUpdateDisable and SilentAutoUpdateEnable settings in mms.cfg to their default values, which are:
If you are running the Flash Player uninstaller as part of your deployment process, redeploy any custom changes that you have made to either AutoUpdateDisable or SilentAutoUpdateEnable.
So make sure you don’t uninstall the previous version of Flash Player “just to be safe” when you upgrade, or at least, verify that the mms.cfg file you use is properly redeployed to your clients after the update.