Here's what I mean regarding hurting the subcontractor.
Let's say we did a modification for painting (Mod A) and a modification for Fire life safety concerns (Mod B). The prime invoiced for Mod B before he invoiced for Mod A. We paid for Mod B and then when the invoice came for Mod A, we want to hold that money because Mod B wasn't found done correctly. From this example, the subcontractors would be different because one would be a painter while the other would be a Fire protection engineer (FPE). So now, the painter is hurt because we won't pay them for the FPE's mistake. I hope that clears up my concern.
By the end of the contract, we are basically finished with everything except these issues. Once these are resolved, I will close the contract...and possibly pursue claims.