There is a VB call, SwapAxis(Axis1, Axis2), that will do essentially that. The one "gotcha" is that it literally swaps the pin assignments, without swapping the motor tuning parameters. So, it will work fine if the two axes have identical characteristics (velocity, acceleration, etc). But, if they're very different, you'll have problems with lost steps or stalling on one or both axes.
The axes are specified using X=0, Y=1, Z=2, A=3, B=4, C=5. So, in your case, you'd want to use SwapAxis(1,3) to swap Y and A. You must then use ResetAxisSwap() to "undo" the swap. Do NOT do two Swaps in a row....
Regards,
Ray L.