I am a German citizen and fly to Switzerland from the US with a layover in Paris, where I need to retrieve my baggage and check it in again. Do I need to go through customs in Paris and if so do I need to pay taxes on items I bought in the US even though I am not really staying in the EU?
Depending on the airlines you're flying with, you might be able to check your luggage in all the way. Call the airlines to check.
If you have to pick up your luggage, then you will have to go through Customs. They might or might not ask you anything. French Customs officers in CDG are notoriously both lazy and aggressive. If they go through your luggage – an improbable but not impossible event – telling them you're just transferring might help, but it's not a very strong argument. Since you're entering the country, there's no way to prove you're not handing over some of your belongings in Paris. Especially not to a grumpy Customs officer.