When you load a saved game file that you have cleared every level, including the lettered bonus levels, Toad Houses will no longer disappear after you take the items. The only exception are the ones that appear based on your timer when you finish a level.

Alternately, if you want to have all of your Toad Houses back, save the game then intentionally lose all of your lives. When you return, all of the Toad Houses will be restored.