The charge pump controls when the motors are enabled - the MX4660 needs a signal to enable the stepper drivers, but it provides a dip switch to generate the signal internally vs from the parallel port. My drive has plastic partially covering it, so it was difficult to move the switch when I enabled it previously. See page 11 of the manual -
http://www.leadshineusa.com/UploadFi...660hm_V1.1.pdf. You will want to turn the dip switch on to generate the signal internally, then the drives will still be enabled when the parallel port is removed from the equation.
I don't think anything bad will happen if you remove the parallel port while the drives are enabled (might want someone else to chime in before you do it), the step / dir pins and any outputs you have will be disconnected (limit switches won't be respected, so if it did move you'd want to be close to the estop / be able to pull the plug). I haven't used a smoothstepper, but maybe disconnecting the ethernet from the computer would be better vs. removing parallel from the driver.
From this post:
Consistent stepper clunking. All axis' all the time, an older computer solved the issue. What kind of computer are you using? I'm using an Optiplex 380.