Does mass flash erase erase eeprom emulated flash memory? Also do I need to edit linker file (for epprom eulation) while uploading code?

[Tesla DeLorean]

Yes the MCU doesn't know you're doing this EEPROM fakery, it wipes everything.

Some STM32 have EEPROM

You should probably exclude areas you're using for EEPROM Emulation out of the Linker's view of what is available to use for application code and data.

[PDhek.1]

Ok. Thanks for the reply.