I have a builder building me a home right now and we had agreed to set up two separate heating and cooling systems for the first floor and second floor of the house. I raised the issue the other day that I hadn't seen the second furnace unit being installed in the attic as agreed. At first the builder said they were going to do that this week. Now he has said the HVAC company thinks its a better idea to set up a 1 unit system with 3 zones. Are they trying cover up their mistake at a discount?
You should have a meeting with your contractor and the HVAC contractor, and have them explain exactly what's going on. Ask them to show you whatever calculations they're using to determine the equipment size, and have them explain how a single unit can replace two units.
It's possible that they're installing a larger single unit, to eliminate the need for two units. This might explain why the price has not changed, though that's complete speculation.
If you're not satisfied with their explanation, it might be time to contact a lawyer.
You and your contractor agreed on duel split systems. However, he contacted an HVAC company who said otherwise and is interestingly, offering a down-sell on this install. (They make their real money up-charging for equipment. So as long as the zoning isn't going to cost big bucks, what's the problem?) My guess is that someone finally got around to doing the manual J and actually figured out the house's requirements and what you guys thought you needed, the HVAC guy says you don't.
If this is a trust issue, you need to do some homework about who you hired; check the BBB, ect.