all you do its correctly define your homing positions
in configuration.h
// Travel limits after homing (units are in mm)
#define X_MIN_POS 0
#define Y_MIN_POS 0
#define Z_MIN_POS 0
change to
// Travel limits after homing (units are in mm)
#define X_MIN_POS -5
#define Y_MIN_POS -5
#define Z_MIN_POS 0
It wont un bump the endstops, but 0,0 will be where it should be when you print
in configuration.h
// Travel limits after homing (units are in mm)
#define X_MIN_POS 0
#define Y_MIN_POS 0
#define Z_MIN_POS 0
change to
// Travel limits after homing (units are in mm)
#define X_MIN_POS -5
#define Y_MIN_POS -5
#define Z_MIN_POS 0
It wont un bump the endstops, but 0,0 will be where it should be when you print