[roofermikeinc]

You should still be holding the final payment. No permit? Inspections?

 

[roofermikeinc]

My problem is WHO do I take my action to?

What you "planned" really doesn't matter now, does it?
What matters is what is written in the contract, in the permit documents and in the Code.
Strength-wise it won't make much difference if they went over an existing 1"x6" plank deck but aesthetically it could be a mess