@lah, there are other topics on losing eeprom/flash content when power to a Photon nears the SMPS drop-out voltage threshold. This has been flagged to the Particle Team but with all hands on the Electron release, things are a bit slow on the Photon side. As for the flashing cyan with quick red burst, do a search and you will find:
I've learned that running any processor via "un-managed" battery power can be a risk as it creates a "brown-out" condition where the Photon can get into a reset loop when power is near the SMPS cut-off voltage. This is something we will definitely need to investigate since it affects both the Photon and Electron.