In PSoC4 we have to use emulated EEPROM component to use flash portion as EEPROM area. One limitation of the Em_EEPROM component of PSoC4 is, it automatically places EEPROM space in flash. This location may changes with different build cycle. This may create an tricky issue during security protection of flash (usually employed for IP protection of your firmware).
As you have to get the address of flash area allocated after a new build and change Flash Security file flags appropriately to allow Em_EEPROM to work within otherwise protected flash area. This is a tedious task and not intuitive as PSoC1 EEPOM component.