I understand the situation. I strongly suspect you are making the right call, but for the wrong reason. That is what I'm working on. "They stacked lumber thus they need an engineer" is incorrect. They overloaded an inadequate 2x6 joist, or, they tried to create a structural 2x12 out of two 2x6's is the correct reason to fail it.
Look at the span tables first, is a single 2x6 capable of spanning this distance? If not engineer.
If a single 2x6 is within allowable span then look at the load, assess its' magnitude and its' location in relation to the support below. If the HVAC's load is out in the span and greater than design load, engineer it.
If the HVAC weighs less than design load for the single joist, or, if the unit is over a support that upper 2x6 is just blocking. Make sense?
In a post above I mentioined that if they have attempted to build up a beam the joint between members needs to be designed to handle the shear. Take a phone book and hold the binding in your left hand thumb under, fingers on top. Grab the right edge the same way and hold it out in front of you flat like a beam comprised of many horizontal fibers. Bend it and notice what happened on the right edge. The fibers slid past one another, horizontal shear failure. Note the shape of the beam. Now set up again but pinch hard on the ends, don't let the pages slide, and bend again. You should feel more resistance to bending and see a slightly different shape. By controlling shear at the ends we have designed a beam that is stronger than one fiber sagging into the bending fiber below.
Historically when framers needed a heavy timber beam of greater depth than available material they would key the members together with horizontal pieces of dense wood or iron spaced along the joint between the two timbers... more towards the ends, fewer towards the middle to eliminate the slip betwnne layers, or, they would sheath the verttical faces with diagonal boards in opposing directions on either face, again eliminating slip. Plywood at both ends of this assembly on both faces with enough nails into each member to safel handle the shearing stress between members with a few blocks across the center to maintain alignment would accomplish the same thing. These are design efforts. Don't forget, I'm a framer, RDP's feel free to correct if I'm mistaken in any of that.