Commerical Real Estate Sale Questions

We are confused with the sale of a commercial property that was completed. The contractor was apparently paid using credits they owed the property manager company ($40,000) based on a deal they had worked out. So the contractor is not getting any money for work completed on this project at all. However, the seller used the contractors invoice ($50,000) for the sale of the property at the full amount with no mention of credits and had contractor fill out waiver for the $50,000 price. They also presented the buyer with a check made out to the contractor ($50,000) for the total of the original invoice. The check was never given to the contractor and was only used to close the sale. We are trying to figure out if this is a normal practice for the sale of a property. Or do we need to dig deeper and get more info? It just seems off to do all of that. Wouldn't it be easier to have an invoice for $40,000 and list the $40,000 in credits, so it washes out to zero? And why would the wavier be needed if the contractor wasn't being paid due to credits owed? I appreciate any help you may have, as this is confusing to us. Does the contractor have to remove the lien since the total is not exact due to credits? The contractor filed a lien for $50,000.
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