OK, since the smoothstepper does not support differential signals, you must be doing the conversion downstream. My swapaxis board simply switches the signals unchanged, taking inputs from two axis and swapping them to the servo drives. The switching is very fast and should be transparent to the system, particularly to the smoothstepper driver.
Mach3 is unaware of the swapaxis board and even 'hot switching' with the axis moving seems to work OK. I have tested the board with the spindle axis active and running the spindle. Switching the axis in this situation simply starts the 4th axis running as the spindle. Switching back does not seem to confuse the system at all. The 4th axis is simply, silently, the A axis again, with the caveat that the position is no longer valid, so indexing requires a re-home. Also a 'hot swap' does not utilize accelleration settings to the axis sort of 'slams into gear' without a clutch . . . so to speak, if you hot swap.
It seems to me that your setup *should* work like this: CNC->SMOOTHSTEPPER DRIVER->BOB->SMOOTHSTEPPER->SWAPAXIS BOARD->DIFFERENTIAL CONVERTER->SERVO DRIVE
Now that you have made me aware of differential step and direction signals being used on industrial drives, I have yet more homework to do. My new 'Super Duty' 4th axis is almost complete and it is not a hobby level machine, so I will need to support differential signals in the accompanying swapaxis board, so I will look into what is needed to accomplish that. Hopefully it will be something simple like dual multiplexers triggered simultaneously.