You are responsible for sticking to your permits. The easiest way to do this is to plan ahead, make sure your daily mileage is doable, and build in extra zeros to help you catch up if you get behind.
If you find yourself behind on the trail and unable to catch up by hiking more miles or skipping zeros, check upcoming alternates. Many alternates are significantly harder than the official trail, but there are a few shortcuts and easier routes too. If this isn’t an option, you should skip ahead to a section of trail where you still have permits.