It should not have changed. G10 P4 S260:260 followed by T4, or vice versa, should turn on both heaters. I'm not sure about M104 S260 because the M104 command was not intended to control multiple heaters.
EDIT: I just checked the code. T4 followed by M104 S260 should set the active temperature of both heaters and start heating them. But M104 S260 followed by T4 won't, because the M104 S260 command will refer to the currently-selected tool (if any).