"Well, your body did think you had been shot through the chest," they explain. "A few of your alveoli went then. Soft tissue is one of the things more vulnerable to this kind of damage. "Best" injury you can take in the Matrix is a broken limb- your mind is hard pressed to make THAT real!
"But I don't think it should affect your RSI. Unless you panic about if, of course- but then thats always a reason to not go in!
"Oh, one thing... I don't want to sound blindingly obvious but try to avoid that kind of punishment again. If you get shot through the chest AGAIN and your real world body gets damaged a second time you may need a longer break."