ChrisM:
I'll do this in point form for brevity:
1. I graduated in mechanical engineering in 1978. I don't remember much of the formulas I learned and memorized in university, but I still understand the theory and the basics. And, in this case, that's all you'll need to understand to realize that you haven't done any harm at all. In fact, I believe you got good advice from the first engineer.
2. As long as you never REMOVED any wood, then you could not have weakened anything. Adding material strengthens the trusses, but where you add it makes a big difference on how effective it is at increasing the strength and rigidity of the trusses. Boxing in those trusses is certainly an effective way of making them stronger, so what you were told makes good sense from an engineering perspective. And, it was important to have GLUED the plywood to the trusses. Nailing or screwing alone would have done little to strengthen the floor. In fact, the screws can be taken out now that the glue has dried, and the floor will remain equally strong.
3. Wood DOES swell and shrink due to seasonal changes in both relative humidity and temperature. Indoors, for example, you can see gaps open up between the boards in hardwood floors during the winter, and close up again during the summer. However, the amount of change in both relative humidity and temperature INDOORS is relatively small compared to that outdoors. It's the much LARGER dimensional changes in wood that occurs outdoors that's the reason why there are separate lines of interior and exterior oil based paints. Oil based paints dry so hard and rigid that they don't have the elasticity to stretch and shrink as far as wood does, so they have to intentionally screw up the film formation process in exterior oil based paints so that they don't dry as hard, and therefore retain enough softness and elasticity to stretch and shrink with wood outdoors. The dimensional change that occurs in wood indoors is quite small in comparison, and in most cases is ignored.
Gaps can develop between the boards in hardwood floors indoors because it's actually the wood cell walls that become thicker and thinner as the wood swells and shrinks. The wood cells are much larger in softwoods, but the cell wall thicknesses are about the same in all wood species. Since hardwoods have much smaller wood cells than softwoods, they swell and shrink more than softwoods because there are more wood cell walls to swell and shrink per linear inch. This is why you can get a 1/16 of an inch gap in a 1 1/2 inch wide hardwood floor board.
(in both cases, wood cells are shaped like long drinking straws with their ends closed off. because of the shape of wood cells, the swelling across the grain of the wood is typically about 80 time as much as the swelling along the grain of the wood. that's simply because there are far fewer cell walls along the grain than across the grain. the importance of this will become clear when we consider plywoods) So, since the wood we're talking about is indoors, you simply have more uniform temperature and humidity, and so you won't have nearly as much swelling and shrinking as you would outdoors.
4. You clad your trusses on both sides with plywood. When making plywood, they dry the plies out so that the moisture content in the plies is typically only about 4 percent. They do this to ensure that the wood is dry enough that the glue will bond the plies together well (cuz glue won't stick well to wet wood). Then, because the grain of the plies alternates, the amount of swelling or shrinking that occurs as the moisture content of the plywood rises again is constrained by the neighboring plies. The only direction that plywood will swell and shrink normally, the way lumber does, will be in it's thickness. It swells and shrinks much less than lumber in width and length simply because doing so requires the stretching or compression of the wood cells in the neighboring plies. Wood is a relatively soft material, and it's quite easy to get it to retain it's shape even though if it were not constrained in any way it would swell or shrink.
For example, in a fir 2X12 floor joist, it's possible to get up to 8 percent shrinkage from fully water saturated (30 % moisture content) to an oven dried condition (0% moisture content). That's a full INCH in a 11 1/2 inch tall piece of lumber. By contrast, when 4 foot by 8 foot plywood underlayment is nailed down to those same floor joists, the recommended gap to be left between sheets to allow for expansion of the plywood (as it's moisture content increases from 4 percent and stabilizes at about 16 percent indoors) is only 1/8 inch. That's about 1/8 of 1 percent swelling in plywood versus up to 8 percent shrinkage in lumber. The amount of shrinkage and swelling that's going to occur in your plywood is very small, and the fact that it's indoors means that the stresses and whatnot this civil engineer told you were going to wreck your trusses and bring your house crashing down simply won't exist.
You don't need to know the rest...
You should understand the purpose of the pairs of 1X3 boards that run perpendicular to your trusses. A 2X12 can make for a very rigid floor joist, or a really springy diving board. Everything has to do with the direction of the applied force relative to the joist. In order to ensure that the joists are most capable of resisting bending due to a vertical applied force, something has to be done to keep the floor joists vertical. The purpose of the 1X3's nailed between the trusses is to keep all the trusses vertical, so they're most able to resist bending from a vertical applied force. Those 1X3's are more than capable of doing that.
As a result, it really isn't necessary to put plywood on both sides of those 1X3 boards. That plywood will also help to keep the trusses vertical, but it's the plywood you're putting on both sides of the trusses that is increasing the rigidity of your floor, not the stuff you fastened to the 1X3's. The stuff you fasten to the 1X3's will only be helpful when there is so much vertical force on the floor that the floor trusses are ready and wanting to twist sideways under the applied force. You won't have that unless you intend to raise a family of pet elephants in your house.
And, finally, you simply cannot con Mother Nature. The way physicists tell if their theories are correct is by seeing whether not things work the way they predict or not. In your case, your floors used to bend a lot. Now, you say they're much stiffer. That is proof positive that the plywood cladding on the trusses is having the desired effect.
I think the first engineer doesn't want to return your calls simply because he hasn't got enough confidence is the stuff he was taught yet. He simply knows the plywood SHOULD have strengthened the trusses, but if you're telling him it didn't, or that it may have had caused some damage to the design of the trussed floor system as a whole, then it's shaking his confidence in the stuff he thought he knew and understood. He's thinking there's other things that he hadn't considered.
I'd carry on cladding those trusses. But, don't bother cladding the 1X3's on either side. That is where you're getting the least benefit from the time and money spent installing the plywood. Do it when you don't have anything else to do with your time and anything better to do with your money than drink and gamble it away.
