You need to unmaximize them and then maximize them again. I don't know if there are any bang commands to help with that... (anyone know? and on a related note, is there anything that will let you restore/max/minimize/move windows identified by handle?)

It's more difficult if you have maximized windows on other virtual desktops, because they'll try to come to the current desktop. Maybe set a flag and remaximize them when you switch to that desktop.