I can answer some of your questions.
Not sure about the VT vs IT, will look into it.
Any and all burnt settings may be overwritten by Mach as they are arrived at.
Your best choice for the B motor is to rewire it so that the direction reverses.
Servo motor run-away or direction reversal methods.
When the polarity of the encoder feedback is wrong, the motor will attempt to run away. The
controller should disable the motor when the position error exceeds the preset following error. If the
motor runs away, the polarity of the loop must be inverted.
Inverting the Loop Polarity:
When the polarity of the feedback is incorrect, the user must invert the loop polarity and this may be accomplished
by several methods. If you are driving a brush-type DC motor, the simplest way is to invert the two motor wires
(typically red and black). For example, switch the M1 and M2 connections going from your amplifier to the motor.
When driving a brushless motor, the polarity reversal may be done with the encoder. If you are using a single-ended
encoder, interchange the signal CHA and CHB. If, on the other hand, you are using a differential encoder,
interchange only CHA+ and CHA-.
Sometimes the feedback polarity is correct (the motor does not attempt to run away) but the direction of motion is
reversed with respect to the commanded motion. If this is the case, reverse the motor leads AND the encoder
signals.
Kenny