If the contractor is telling you that his deviation has enough capacity, tell him to prove it to you. You already designed it once, so if you have to check out this deviation, you should also get paid to do it. Why should you have to do free engineering for someone elses screw up? I would inform your client of what the contractor did, letting it be known that what happened was an unauthorized change by the contractor. Let your client know how much your fee will be to either check the adequacy of the change or to review any "proof" provided by the contractor. If your client (the architect?) seems willinig to let the matter drop I would let the code official know.
If the Simpson connector provided by the contractor has been fabricated for bolts (large holes), I don't think there's any way the connector assembly is going to be adequate by substituting screws for bolts. I would never approve it. Again, why should you accept the liability for something the contractor did that is not in conformance with your design? If this thing fails and someone gets hurt or killed you could be in for a lot of trouble.
It is the contractor's job to build the structure, not to re-engineer it. If the contractor wanted to substitute a different connector than the one you specified, the contractor should have requested the substitution in writing to you before building it. To sum up my wordy response, in my opinion the contractor doesn't have a leg to stand on. When I am made aware of an unauthorized substitution, I always make them remove it and furnish and install what I specified. If it's not feasible to do that, then I make sure that I get paid to engineer a fix for the problem the contractor created. The costs to implement the fix should also be the responsibility of the contractor.