It is per night stayed whether free or not. If you have used an upgrade the offers won't make sense. However, you can go back to the estandby options after the upgrade has been applied and get a new set of upgrade options. Use the original link.

I did this with Mayakoba after applying a suite upgrade. But at check in they offered me only the original upgrade options and said that was all that I was allowed. So it is hit and miss.