Arduino as ISP erases EEPROM

I'm working on a project which uses a Mega2560 programmed via the SPI interface. (The Serial interface is not available for programming).
The device is designed to use the EEPROM for long-term storage of various information including calibration data. Unfortunately, IDE clears this information when loading a revised program. I'd like to modify the IDE to preserve the EEPROM contents when reprogramming - avoiding re-calibration would certainly speed up debugging. I very much wish to avoid running avrdude manually.
Thank you for any help you can provide.

The 3rd party Arduino boards platforms MegaCore, which provides support for the ATmega2560 microcontroller of the Arduino Mega 2560, allows you to configure the EESAVE fuse setting via the Arduino IDE's GUI when you have a MegaCore board selected from the IDE's Tools > Board menu. The behavior you desire would be achieved by selecting Tools > EEPROM > EEPROM retained.

You can learn more about MegaCore and find installation instructions here: