Bill - sorry, I should have made that more clear.
The new "US Topo" is a completely new tileset in a different map projection. So, yes, you will be starting over from scratch. There's no reasonable/good way to combine them, unfortunately. Any old maps you had downloaded will still be available, but only as their own tileset in the old "Topo 2M, Topo 4M, etc" tilesets.