The seemingly universal solution to this situation is to scour the earth for thinner and thinner parallels in the quest to eventually find the perfectly thin parallel that will prevent you from ever having this experience
Relax - there's a simpler solution... with a simple trick I learned from my journeyman and a little forethought, you'll never have to worry about damaging your parallels again (at least not with a drill bit)
Step 1: The Trick
Make sure you have parallels that are slightly thinner than the parallels you are going to rest your job on (by 1mm or 2mm)
Place the wider set of parallels right up against the sides of the vice
Then place the thinner parallels on either side of the block you are clamping.
Finally you should use a rubber dead weight hammer to tap the job onto the wider parallels checking that they are held tightly by the job clamped ontop of them
This should ensure that your job is resting only on 1mm or 2mm of each parallel once the job is clamped allowing you to drill away to your heart's content without having to worry about hitting a hardened parallel