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The SFLASH does not get automatically erased when you program your device using PSoC Programmer. It is possible to erase SFLASH memory in each programming by using any of the two methods given below:
1) You can make use of the CySysSFlashWriteUserRow() API to write 0 to the desired SFLASH rows at the beginning of each program. This will be same as erasing the SFLASH.
This can be done for all the four flash rows.
2) You can also use the SFLASH Update tool which gets downloaded as a part of PSoC Programmer to program the SFLASH.