It depend on the reason why the first colony dies as to if you need to clean the hive. If the colony died from starvation is different to them dying from a disease.
A few major things controlling if you get honey, or how much, is the strength of the bee colony and the availability of nectar for them to feed on. To a lesser extent is the number of bees in your hives area competing for the available nectar.
A common mistake made is that the super is put on too early, before the colony needs it and it sounds like you have made that mistake. The brood box should be really busting with bees and at least 80% of all the cells in the brood box containing brood, honey or pollen.
When a Flow Super is added the first thing the bees must do is to seal up the cracks in the cells then if the conditions are right and there is no cells available in the brood box to store honey then they will use the super. When you lift a frame from the brood box is it really covered in bees? A few photos would be a great help.
That may be your problem, not all species of bees are suitable for having in a bee hive and producing excess honey, you really should at least know what species of bee you have then do some research if they are suitable.
Cheers