Insulate the existing returns. Don't downgrade to flex.

UV won't stop mold in a return. It will raise maintenance costs as then you have to replace UV bulbs annually. They may create ozone, which lead to health problems. (gadgets rarely fix anything, other than poor boy bottom line. These gadgets are a billion dollar industry.) Mold production is typically around the indoor evaporator coil, not the return unless it's an electric air handler (mold growth requires moisture). What you probably see is dirt. Calling that mold would require testing. You send specimens off to a lab. They then tell you what it is. Guessing never goes anywhere fast. In some situations an HVAC system may "sweat" in various locations, under certain conditions. This moisture can grow mold. Because this is a "facility" I think you need to tell us more about the HVAC system for this particular unit that your folks live in. What kind of system is it? Mod # / Ser # of the equipment. Name of the equipment, are there outside individual condensers that you can see? Take some pictures and post them.

In addition to painting the vent cover to match the wall, painting the interior of the duct (just the part right behind the grill) makes it even less noticable. While you should definitely seek out the advice of a professional, I wouldn't remove any of them. Our first house was built in 1910 and thus the forced air system was added later. It had inadequate returns and it was impossible to get the temperature to be the same throughout the house. It was very annoying. Since your house is only 11 years old it was probably built state of the art at that time which is a good thing.

I always think this might be causing the issue why my 1st floor is not cooling because when I turn the AC on the 1st floor the return air duct on the 2nd floor is sucking the air.