Hi,
Could you please specify the target MCU you are using?
In case it is S12(x) family there is an option to enable/disable erasing of EEPROM (go to File -> Configuration dialog - where you can specify which flash memory blocks should be erased:
stanish_0-1709902761322.png
If you use S12z the debug will erase just Program FLASH. in order to program EEPROM you should use Flash Programmer component (Target Task):
stanish_1-1709903067485.png
Hope it helps.
Stan