If we save things with EEPROM and then update the device firmware, will the EEPROM data still be available?
Yes, EEPROM data will be unaffected by a application and/or device OS update.
The memory map of the device you use will show that EEPROM not located within the memory blocks where firmware modules reside
https://docs.particle.io/datasheets/boron/boron-datasheet/#memory-map
https://docs.particle.io/datasheets/wi-fi/photon-datasheet/#memory-map-common-
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