Thank you!

I need to lower 2 toilet flanges about 2 in. One is PVC the other copper, but both 3 in. I think I need to remove the old ones, cut the pipes and add a new flange. Is this correct? I think the new flanges will have to go inside of the 3 in. pipes. I hear that this is not ideal. Why is this? Is there a better option?

"I need to lower 2 toilet flanges about 2 in. One is PVC the other copper, but both 3 in. I think I need to remove the old ones, cut the pipes and add a new flange. Is this correct?"
That's right, unsolder the brass flange from the copper stub up and clean and save it.
"I think the new flanges will have to go inside of the 3 in. pipes. I hear that this is not ideal. Why is this? Is there a better option?"
I prefer a outside flange if possible. The larger diameter opening on a outside flange gives better drainage. Good luck, Tom