We just replaced the tile in the bathroom - should the flange sit on top of the new tile or be recessed and flush with the top of the new tile?
Normally the flange sits on the tile. When the flange is lower, you can buy a spacer kit that will raise the flange up to it's proper height.
The problem with a lower flange is the seal. A standard wax ring will not reach both surfaces and seal the connection. This allows water and sewer gas to leak out.
They do sell oversized wax rings, but I like to use the spacer kits as it keeps the space close to the original.
I take it you kept the original flange because it was a lead one?
"They that can give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety."
B. Franklin 1759