I am removing a wall between the living room and kitchen. It has 2 stud cavity return vents on one side and one on the other. Since these will no longer be available can I replace them, on the main trunk below in the crawl space, to maintain enough air flow

You will have to put them in an other wall or in the floor. Lack of sufficient duct is the single largest cause of premature heater or air conditioner failure.

Do you really want to suck out from your crawl space? As Grady says, move to another wall or use a floor return.