Hey,
Since the drive uses the A quad B pulses to know the rotation direction ( as mentioned before ) it is important that the pulse timing is OK, and therefore ,if possible, checked by the drive.
There is very little chance that rotation direction is detected wrong. I had it once in my 25 years of working with drives, a 550kW DC motor on a GE Siltron drive went running full speed backwards when given a small forward reference.
So switching off the detection gives a small risk, but damage to your installation can be severe in some cases. I think, in your case, there will be some damage if the motor is running the wrong way. On the other hand, if the fault detection is too sensitive, as mentioned by rdrast, , there will be not much of a choice if you want to run this system without daily resets.
Greetings John.