It is not recommended to place Em_EEPROM component in user SFlash region. If you would like to store custom data in user SFlash rows, please use CySysSFlashWriteUserRow(uint32 rowNum, const uint8 rowData).
Thank you for your reply, Could you introduce a way to keep em_eeprom data while updating the program?
The Emulated EEPROM Component emulates an EEPROM device in the PSoC device flash memory. Hence, Erase All Flash step in the programming flow will erase Em_EEPROM contents as well. \
If you can use bootloader-bootloadable architecture, the bootloading step will not perform Erase All. It updates bootloadable area of flash, row by row. If the user forces Em_EEPROM data storage in a checksum exclude region, Em_EEPROM contents will be retained. Please refer https://community.cypress.com/docs/DOC-10254 for more details.