That is my next step in debugging this issue, is to get rid of all of the other EEPROM.Put()'s and start working backwards. I may go as far as starting a new project that does nothing but read/write to the EEPROM to try to reproduce the issue in a separate project.
Here is the link to the article that had info on how to dump the EEPROM to a file: https://community.particle.io/t/eeprom-values-wiped/16568/4