I'm doing Zelda as an app. What system should I use for map updating? The map data will be in the app. What of the following two systems should I use:

1. App copies the data directly into RAM, and plays with that as the map. If the map has changed when it is put away, I need to unlock flash and write the new data back into the app directly.

2. App copies the data into an appvar, then uses the appvar as the source. When playing, the game copies data from the appvar into RAM, not from the app itself. If the data need be changed, the appvar is updated, but not the app. (this option enables reset...1 doesn't).
I think the second option is better, because if you mess up while unlocking flash you can do very bad things to a calculator, such as deleting the certificate. Also, it would let you transfer the app between calculators without resigning the app.

EDIT: You can also create a hidden appvar, so it will be less likely that it would be deleted.
Thanks. I do prefer that option.

PS: Would you really have to resign if you do that?
Yes you would have to resign the app in order to transfer it if you modify it.

That said unless you are doing something crazy like a gameboy emulator or a flash drive reader its best to pretend that flash cannot be unlocked. Flash unlocking was made hard by TI for a reason, you don't want to be messing with it if you don't have to.
  
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