Good design for reading a DIP Switch once
Everything here assumes the switches are connected between microcontroller pins and ground, so that a closed switch reads zero.
Option 1:
Drive all your pullup resistors from a microprocessor pin.  This'll take an extra pin, but when you're done with it you can pull it low.
Option 2:
If you have a modern microcontroller, it has every kind of pull-up, pull-down, etc.  Usually the pins will be inputs on start-up (check the data sheet).  Assuming the processor allows it, set the pins to inputs with pull-ups.  Then wait a bit, then read your switches, then set the pins to pull-downs or as outputs and set them to 0.