You should probably program the inputs attached to the parallel port with appropriate pullups and pulldowns so they assume a well-defined state when you disconnect the cable. That way your circuit will stay in a well-defined state and won't possibly do something such as turn on the RAM or microcontroller and then try to drive against them with the FPGA.

The I/O pins of the XC4000 have pull-ups and pull-downs that you can enable to hold the pin high or low when there is no active external driver present (such as when you disconnect the parallel cable).

Note that the two least-significant data bits of the parallel port pass through 74LS14 schmitt-trigger inverters before reaching the FPGA. So you don't have to pull these FPGA pins high or low; as soon as you disconnect the cable the inverter inputs pull high and their outputs to the FPGA go low.