Loot's told me I need to clean Enhanced Lights and FX, but when I Apply Filter for Cleaning it gives me three warnings with these headings: Warming Ununsed data in

What do they mean and what do I do next?

The rest of the message may have been helpful ..

But I am guessing this is just the unused data in skyrim.esm which can be ignored

What you do next - Carry on doing the automated cleaning http://www.creationkit.com/TES5Edit_Cleaning_Guide_-_TES5Edit#TES5Edit_Cleaning_Instructions

Edit : there is also a bit of manual cleaning of the master files needs to be done if you have not done it .. See the guide link in my sig.