Well the system is actually a 10ton unit it has two 5 tons and both of the coils go to one airhandler. the top unit is completely plugged even the fan had a nice layer of dirt. the hole is the "custom made" filter rack for the system. its on the return line just before it goes to the coil.
I thought you were saying a whole in the line set, like a leak. Now I see, said the blind man.