Not really, and not with that library. The library effectively reserves a row of the program memory storage space and then rewrites the data in that row every time you update the stored data. However, re-uploading will reset that space to the default values.
The MCU does support emulated EEPROM and in Atmel Studio ASF has a library for this. It basically reserves certain sections of the program storage space for the emulated EEPROM. This is done through the device fuses, you also have the option whether to wipe that area each time you program the device.
Getting this to work with Arduino would be difficult. Additionally, it would likely require some modification to the bootloader.