For this explanation, callbackFcn1 is the initial callback function and callbackFcn2 is the one that should terminate the first one.
Create a binary flag in your GUI with a default value of false. callbackFcn1 will run as long as the flag is false and there should be lots of checks within callbackFcn1 to determine if the flag is still false. If the flag ever becomes true then two things should happen. 1) use return to exit the callback functions and 2) reset the flag to false.
callbackFcn2 merely sets the flag to true which tells callbackFcn1 to stop at the next check.
Notice that you can only stop callbackFcn1 at check-points to put them in strategic places including within loops.
This answer demonstrates this process in AppDesigner but the same logic is true for GUIDE GUIs.
