It may not be as simple as just flipping teh X/Y. IF you have changed teh orintation of XY from the way the OEM built it then ALL of the positional values of the tool change macro may be wrong for the way you want to run the machine. You may have to start from scratch and find all teh new values as well as change the directions of motion.
Normally all tool change values are in machine Corrds and are based on the relation to the Machine's 0,0 point when Referenced Home.
You also may find the Toolpath display will be wrong as well as where Home is located.
(;-) TP