He argues that because all the CO2 in fossil fuels originally came from the earth's atmosphere. Then there can't be a problem releasing the CO2 back into the same atmosphere.
Intuitively it seems obvious to me that the quantities CO2 was stored up over a long time and now is being released back into the atmosphere in just a few short decades, which is causing problems, but his counter is that the earth is a closed system and so the total amount of carbon CO2 is constant. This part I'm less sure on but I have a feeling he must be wrong on that too.
Can someone please explain where the flaw is his logic is? I want to debunk this in as scientifically accurate as way as possible.
Let's go with a simple allegory:
Say, your friend had a pickup-truck (sorry, in my mind deniers all drive SUV or pickup^^). He uses it to transport a lot of material, e.g. paving stones. He knows, his truck is able to transport the total amount of stones (because he tried in the past, or because the specifications say so, or because someone told him, doesn't matter - like we know that earth's atmosphere held a lot more CO2 back in the day).
Is he going to just dump the whole load at once from 2 m height into the back of his truck? I doubt so, because that would at least put some dents in the truck, or might even break the springs or an axle.
He'd pack the stones there manually and use enough padding to make sure nothing gets damaged or slips during the transport.
Currently we're dumping the stones all at once - and we'll surely break the vehicle, if we really continue. Earth, like the truck, needs to adapt to changes. And, as we know, geological timescales are a lot longer than we can truly observe - thus the current changes, though stretching over several generations, are way too fast for earth to really adapt.
Third: While earth is a closed system, states within a closed system may change. Say, you have a terrarium with some mice and a lot of wood. Then you burn the wood. The mice might survive the fire, but in the end will suffocate, since there is a lot more CO2 in their atmosphere now.
So, yes, releasing trapped carbon from fossile fuels and whatnot to the atmosphere doesn't change the overall mass of system earth. But it changes the state of the system - and we are depending on the current state of the system.
Also - I know, this is not scientifically - say we are wrong when it comes to greenhouse gasses, and he is right. What if we undertook a lot of effort to not to produce them, to clean our environment, to create less waste? We'd wake up one morning and be "Dang, we made our planet worth living on again, how could we?!" - Or, as one of my professors put it: "Would you get on a plane when there is a 10 % chance, the plane is going to crash?"
In this situation, both your body and the Earths atmosphere try to radiate in the infrared, but with a blanket that heat cannot escape anymore. No matter if the blanket was laying around somewhere else for thousands of years, in that moment it gets warm.
This is of course a flawed analogy, the better one is the one of the greenhouse: Visible light can enter, providing heat, but cannot escape in the infrared, because the glass is intransparent to infrared. The more $\rm CO_2$ there is in the atmosphere, the more 'glass'. No matter if this glass was buried underground for ages, at this very moment it causes temperatures to rise enormously.
Same story with why a car heats up into a death trap in summer, while the exterior of the car at the same moment doesn't.
Your friend (and probably other climate denialists) confuse the Earth's mass balance with its energy balance. One doesn't have much to do with the other.