Is there any way to not connect pads to a shape if it will cause DRCs?

I had a request to gnd flood internal layers after routing was complete, but it created some issues I haven't fully been able to solve. The main one is that unused pads are suppressed during the design, but then when the gnd is poured suddenly there are a lot of pads that didn't used to be on that layer that now interfere with traces. Is there any way to easily fix this at this point in the design? I know I could do voids around problem pads but there are over 100 on my relatively small test board so it doesn't seem like a good use of time. Not suppressing the pads earlier in the design isn't an option because I need that space for routing. I played around with clearance values but some of the gnd pins are 60 mils and putting a clearance large enough to prevent those from connecting to the shape is excessive and cuts off unrelated shapes that happen to be near a gnd thru hole. Any insights are appreciated. The gnd flood is a manufacturer suggestion not design critical so I'm not too worried about it if there isn't a good resolution but I want to do my due diligence.