Your program should let you know what to do. Pads get stolen all the time, I wouldn't worry too much about it. The worst case scenario would be a forged script that actually gets caught, and then you have to waste an hour in court to testify that it was indeed fraudulent.
My attending got a call last week about a stolen script pad, from a vigilant pharmacist concerned about an unusual spelling/dosage:
"Mophine, two pounds".
Nothing like a good two pounds of mo'phine in the morning.