The lien waiver signed by the GC likely does not preclude a lien filed by a supplier.
Further, the lien waiver signed by the GC likely represented that the GC had paid all subs and suppliers. That misrepresentation may violate the consumer fraud statute.
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The supplier may have a lien, however, for the roofing contractor to recieve your funds and not pay off the supplier, is a criminal act - contact the disctrict attorneys office or law enforcement (police/sheriff) to determine if they would pursue criminal. No guarantee for you at all as lien my or may not be released, depending if contractor has resources or not to try to remedy, but criminal is obviously the largest hammer to the contractor's head.