To avoid lost steps from the stepper motors, you will need to consider a motion control board and not use the parallel port.
This really has nothing to do with lost steps. Thousands of people use Mach3 with the parallel port without losing steps.


Whatever you do, you will need to use an external motion controller because there is no way to get the encoder signals into mach3 without one.
You can get encoder signals into mach3 through the parallel port. You'd probably need a second port, though, as one probably won't have enough inputs.

But regardless of whether you use a parallel port or motion controller to get the signals into Mach3, Mach3 can't do anything with them, except display the values in DRO's.

The motion controllers that can close the loop with Mach3, do it on their own, and Mach3 never sees the signals.