In my opinion trying to close the loop is a waste of time with steppers however updating position from encoders after manual movement should be possible without any hardware.
I was interested in doing something similar a while back, instead of linear scales I was wanting to use my servo drives encoder outputs. Problem with that was I could not get the hardware I was using at the time to accurately read the high counts from multiple encoders. As you will be using much lower counts from the linear scales you likely wont have that problem even if being input via the parallel port.
Anyway what I had was some VB which, when I pressed the Reset button, looked at Machs position and encoder position and it would then pop a message up if they were different. It would tell me what the differences were and ask if I wished to update Machs DROs to encoder position.
Hood