I find it very difficult to believe that any building inspector gave a CO on a promise that something was going to be done later. By that logic, all new buildings could get their COs before construction even begins.

Get a lawyer who knows Zoning issues in the town...and one who's politically connected.

I suspect the town can revoke a certificate of occupancy. The first one may have been granted after the builder said that the perk and deep test were conducted, or there may be other issues at play. But towns revoke certificates of occupancy all the time. Usually it's because something has happened in the interim. In this case, if those items were required of the builder and were never done, the town probably is justified in its action. However, you need to get a lawyer to clarify matters for you and, if appropriate, fight the decision.