Atmel datasheets specify that the flash memory endurance is 1000 write cycles in normal mode and thru SPI, if possible. What will happen after that?

My solution is to had off my chips to production now and then. Once a chip is shipped in a product it is unlikely to be reprogrammed more than once or twice. As a student, you may be able to "trade" the chips with someone making "permanent programs"

Anyhow the endurance limit is not founc by programming and erasing 1000 chips 1000 times, it is a value found by stressing the chips and calculating the value. You MAY get 5000 reprograms from a 1000 endurance chip and you may not.

Erik