There’s nothing to our knowledge that would intentionally erase EEPROM, this is some kind of bug, either in the application code or in the eeprom code itself. (We are emulating eeprom in flash memory so it’s a lot more involved than simply writing data to memory.)
When this happens again, please connect the photon to a computer with dfu-util installed and run
dfu-util -d 2b04:d006 -a 0 -s 0x800C000:0x18000 -D eeprom.bin
and send the file, and I’ll investigate. Thanks!