I am successfully fetching Apple APNS feedback data via PHP. The structure that I am getting (after some processing) looks something like this:
timestamp
device
The timestamp is the crucial element here. The timestamp sent by Apple indicates the last time the push service attempted to deliver a message to the device and found the app to be uninstalled. If the device has re-registered with your service since then there is no need to delete it.
Therefore, every single time your app loads and sends the token to your service, you should log the time in your data store. When you run feedback you should check the time from Apple and compare it to the time you last received an update from the app on the device. If the time Apple sends is newer then the time you received an updated then you should delete (or disable) the device. If the time from Apple is earlier then you do not need to delete it because the user has reinstalled the device since Apple last tried to deliver.