Upper Crust franchisees are lashing out against the pizza chain’s owners for selling thousands of discount vouchers on Groupon without their knowledge, keeping the proceeds, and then filing for bankruptcy protection.

Independently operated Upper Crust restaurants in Newburyport, West Roxbury, and Portsmouth, N.H., said they will no longer honor the website deals because they never received money from the Boston-based pizza company to support the promotions. The franchisees are not part of the bankruptcy and are still open after a trustee on Monday night shut down all 10 company-run restaurants across the region.