Yes, you are correct, the number is limited........TO ONE MILLION!

To quote the Microcontroller Manufacturer:

" High Endurance FLASH/EEPROM Cell
- 100,000 write FLASH endurance
- 1,000,000 write EEPROM endurance
- FLASH/Data EEPROM Retention: > 40 years"

The FLASH is used to program the chip..it can be re-programmed 100,000 times.
The EEPROM is where the settings are stored and only written to when changes to the settings are made.

I don't think you can wear it out in your lifetime!