Since the encoder is square wave not quadrature, do you have to stop first before changing directions for proper measurements?
In other words, if you are commanding along in one direction at some low speed like 50mm/s or less and want to change direction to -50mm/s, would you first need command it to zero and wait for the encoder to read 0 speed, and then command the reverse direction, in order to get as accurate as possible encoder readings?