I am not familiar with the Atmel; however I am fairly sure that the principles from the Philips/FlashMagic apply for Atmel/flip.

What you need do (if you want a partial update) is to segment your application since no flash segment can be updated without an erase. Every function must have a pointer to it at a fixed neverchanging address.

Then when routing all calls through these pointers, you can accomplish a partial update.

After all that said, WHY? it is deade easy to update it all why this interesst in a partial update.

Erik