Is it dangerous to drill through an infected dental crown to do a root canal?

I have an ill-fitting dental crown that's been in place for about 7 years. Because it doesn't fit properly, there's a huge gap between the crown and the gum line. My endodontist suspects infection, and he's going to redo the root canal by drilling through the crown. If there's a lot of bacteria inside the crown itself, could drilling through the crown cause that bacteria to be pushed up into the canals?