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Could you share more details regarding your application? Please let us know if your end application requires two versions of hex file, one wich supports partial and another with full programming of 2KB EEPROM memory.
The end application only needs 1 version of the hex file that supports a partial EEPROM. I would like to have a section of the EEPROM reserved for things like serial number, revision of the board, initial firmware, and similar data. I don't want to lose that information when I reprogram the PSoC. The hex file's EEPROM section would include common settings like PID loop values that can be reset after programming without causing any problems.