Andy is correct. What you are describing is In Application Programming, or IAP. And in fact some derivatives do include calls or instructions to directly erase and write to the EEPROM/FLASH memory. For example, on page 103 of Atmels datasheet for the T89C51RB2/RC2 one finds

In-application Programming Method

Several Application Program Interface (API) calls are available for use by an application program to permit selective erasing and programming of Flash pages. All calls are made through a common interface, PGM_MTP. The programming functions are selected by setting up the microcontroller’s registers before making a call to PGM_MTP at FFF0h. Results are returned in the registers. The API calls are shown in Table . A set of Philips ® compatible API calls is provided. When several bytes have to be programmed, it is highly recommended to use the Atmel API “PROGRAM DATA PAGE” call. Indeed, this API call writes up to 128 bytes in a sin-gle command.

You can find the datasheet at this link.

http://www.atmel.com/dyn/resou...oc4105.pdf