Movie TF's apparently have no problem with missing appendages. I mean watch ROTF, Starscream casually reattaches his arm while having a conversation with Megatron haha
i dont think they would replace optimus's arm,if they'll do that im sure,they'll also do that to his other arm,and even if its just a plain arm,im sure it will have random weapon coming out of it.
His arm is still on one piece so I would imagine Ratchet can just effortlessly reattach it. Starscream was able to snap his back on in ROTF.