If you use AvrDude directly to upload (via ISP) it most likely will send the .eep file by default (never taken notice of EEPROM behavior via ISP) overwriting the EEPROM data. The IDE does not do this so the EEPROM data is persistent between uploads. You'd have to make sure you do not re-send the .eep file if you want to keep the data.
Also there are commands in AvrDude to read the flash contents, I'd assume there is the same for the EEPROM.