If you clean it this way - using a soaked paper towel as opposed to spraying the WD40 on the chain and letting it drip through - you really don't need to re-lube the chain. All you'll be doing is cleaning the outside of the chain, not the inside. In fact, this is what I, and a lot of people do routinely. It's only the lube inside the chain that counts. I actually thoroughly clean the outside with a rag soaked with mineral spirits when I lube and/or just wipe down the chain.As JCavilia said, you could just wipe the chain thoroughly and be done with it.
Or, you could spray a folded paper towel with WD-40, then wipe the chain. Repeat as necessary until the Tenacious Oil is removed to your satisfaction. Then lubricate as usual.