It depends.
There are controllers that work with Mach which will do that. The CSMIO/IP-A is one and I think Galil, DSPMC and probably Kflop with K analog also.
The one thing they all have in common is they control analogue (+/- 10v) command drives/amplifiers. There are Step/Dir controllers that update Machs DROs from encoder position, the Hicon being one but I am not sure if it actually closes the loop itself or just uses the encoders for position update.
The CSMIO/IP-A controls the analogue command to the servo drive to keep the axis on course, it knows the position by reading the encoder from the motor, it then updates Machs position DROs with that information. Even if the servo drives are disabled the DROs in Mach will always be updated even if you rotate the motors manually, assuming of course that the encoders are still powered.
Hood