Hey. You’ve get same motor model as me 
I’ve got same encoder as yours(it’s different from maslow default encoder). It was working good for 3 months and now it started to miss steps.
I want to discuss this problem here Minimal encoder resolution
Imo the best way is to get diffrent encoder board or go for optic encoder.
I re-soldered connectors to bigger raster 2.53mm then added 4x1 shielded cable for encoder and 2x1 to directly to encoder.
It does help till yesterday day i found out bit is going deeper then it should.
Your hall sensor is just two hall sensors in one case. 4 pin wersion of dual hall sensor.