i've always sent my macs in for repair just the way they are, upgrades and all, and have never got macs back with any problems. if your at the genius bar, they usually write down a few notes about your computer while they are creating the work order. all you have to do is tell them to make note of your upgrades so it reflects in the paperwork they give you before you leave them with the computer. if your setting up a repair over the phone, just let them know you upgraded your memory and hard drive and to make a note of it. if you get the computer back with anything less then you gave them, then at least it was noted in the paperwork and they'll resolve the situation quickly. its really that easy.