Emulated EEPROM

2 Questions:
1) Does Emulated EEPROM work on XMC4000 family?

2) I'm using E_EEPROM app on a XMC1302 device. Seems to work well.
When programming or updating a device, how can I preserve the contents of the EEPROM? I have cal data stored. It seems if I update the device using Dave and debug, the data is preserved. But if I use flasher app, XMCFlasher.jar, the EEPROM gets erased.
Any help is appreciated.