I wouldn't completely eliminate the intake. But i would cut it back to 60CFM max. And just leave it that it only opens when the heat or cooling is on.
The HVAC installer wired the intake direct to the blower motor I believe so that the intake opens whenever the fan runs. He completely bypassed the Honeywell Y8150 controller so I assume there is no way to cut it back to 60 CFM. How can I get the schematics to find out how to re-wire properly and how would I have it come on whenever the fan comes on and use the controller. The controller has no such option I thought?
For the carbon filter pad, it hadn't occurred to me that it could get sucked away. I just thought using some HVAC foil tape would hold it, but I guess not. So my only option is to have a cutout made for a carbon filter frame? How much might that run and how would that work? They cut it out and somehow make a door for a filter to be installed? Sorry for having so many questions, I am really confused by this all.