I undertand that when that valve is ran "all the way down" that the line is then completely blocked. But, apparently not to the little nipple where you attach the line to the Freon tank. I keep a cap on these nipples to prevent freon leakage.

I want to replace the Schrader valve in the charging nipple but don't know how to block the flow of Freon through the nipple. How do I do dat????

There is a process that will let you do what you want to do on your particular unit but, I am hesitant to go into detail on that process here. It can cause serious damage to your unit and you personally if you don't have the knowledge and experience with the process.

I'm concluding you are suspecting a minute leak at the Schrader Valve. If you take the cap off the service valve and look inside the cap, there should be a doughnut shaped rubber seal inside, at the top. If there is non or, the rubber is deteriorated, you can replace it. If someone were to come into my shop and want one of these as a replacement, I would give them one for free. Perhaps you might have a shop nearby you could ask for one. Otherwise, what I would suggest is to obtain an "O" ring that will fit into the top of the cap and will seal around the outside edge of the valve. You don't want a solid piece of rubber because as you tighten the cap, you stand the chance the rubber will distort and push down on the valve. Make sure the cap is on tight but don't over-tighten. Unless you have access to refrigerant oil, don't put any oil on it, just leave it as is and you should be good to go.