We understand the frustration with some of the limitations in the map caching feature. We are using a 3rd party library to handle that. We also have to apply some limits to the caching otherwise we would need to charge a lot more for the app.
1. All the map tiles get stored according to their original URL. When the app makes a request for a URL that it already has in storage it will use the stored one instead of downloading a new one. The files are all there in the same place. Map Pilot doesn't make any distinction between redownloading the files or not.
2. All presses of the save map button count towards the 10 sample map caches.
3. You can continue to save new missions past the 10 sample map caches if they are based on tiles that are already downloaded.
This could all be avoided by simply signing up for your own Mapbox account and getting your own credential. It only takes a few minutes and could probably have been done in less time than it took to write this post! :)