There is probably some double geometry left (if you have two Faces on top of eachother and then try to ALT+S scale one, it can only go in one direction, if that makes sense).
Select all (with A) then M > Merge by Distance. Just to be sure, also (with everything selected) SHIFT+N to re-calculate the Normals.
(By the way, those are the top two problem solvers, that will solve a lot of your modeling issues.)
Now it should work as expected (you might need to seperate some pieces, I honestly can’t remember, because the whole top is one piece now).