I'm still a bit rusty (read: haven't built a model in about 17 years) and was afraid to grind away the inside right up to the point where I could see the exterior(afraid of working the plastic after it was already that thin).
Using a drill approximately the same diameter as the flood hole I drilled out one end of each flood hole then gound one long trench along the inside using the drilled hole as a depth gauge.
Once I was close to the the thickness I wanted it was really easy to remove the rest of the flood hole by drilling the other end then scraping/filing the insides. I also used a bullet nosed stone to slowly grind away from inside if I found the finished flood hole edge was still a bit too thick.
For myself the piece of mind of being able to see how deep the trench was allowed me to be a bit more aggressive in grinding the trench. For myself the drilled ends looked nice and uniform.