We've seen the same problem, the EEPROM being written over with FFs at power down. A simple fix is to use something like an STM1061 Low Power Voltage Detector. Our sytem runs off many different power sources, many of which drop voltage slow enopugh for the Photon to go nuts and overwrite the EEPROM.
There are many choices of threshold voltages for the STM1061, so you can do whatever you want to setup the threshold point. The parts are very cheap (about 42 cents), small, and easy to get.
When the voltage drops, the 1061 senses it and pulls down on the reset line, preventing the Photon from doing its dirty deed.