I2C EEPROM endurance
The endurance is in write cycles for one cell.  

If you fill the 4096 byte EEPROM once, you still have 999999 write cycles left for each cell.  

If you (over)write the same byte 4096 times, you have 995904 write cycle left for that particular byte and full 1000000 for each of the rest of 4095 bytes.