If I update the firmware on my HARDY 4000 series unit will I loose my calibration?

You should not lose the calibration or any of your settings.  If you have any concerns about this, remove the SD card from the unit before upgrading it.  Once you have the upgrade completed, you should cycle power on the unit.  When the unit is powered down, insert the SD card back into the unit.  When you power up it will read all the data, including the calibration, from the SD card.