There used to be a cautionary note in the README for v1.0d that the default GRBL settings are loaded on first flash due to new memory items ($30, $31, and $32) being added. Maybe that was lost going to 1.1.
From the GRBL FAQ for 1.1:
"After flashing, Grbl tries to check the settings in EEPROM. If it finds an incompatibility, it will automatically clear the EEPROM and restore its default."
An Easel machine setup should reset the GRBL configuration to the Inventables default values for your specific machine size but if you've calibrated your X/Y/Z motion, you'll need to re-enter that manually.
I've not yet tried the upgrade on my Xcontroller, this is all "in theory".