So I have flashed the dual end-stop Marlin version to the ramps 1.4 controller of my MPCNC.
When I open Estlcam it tells me that it is not compatible with 3rd party firmware and prompts me to flash the board. Does this over-write Marlin? Do I lose all the configuration.h changes that I made to support the LCD screen etc?
Sounds like you are opening the CNC version of Estlcam. We cant use that with Marlin or the Jackpot boards. You need to open the CAM version of Estlcam. The docs show deselecting the CNC side when installing but many people miss it. I forget all the time when I install updates so I just delete the icon for the CNC side