First of all, you gave us wrong information about your problem. See, what the first comment you get is.
wait, did I read it correctly? PCI slot?
surely will damage it.
You were mentioning PCI slot two twice. I know the other would understand what you mean, if.....that's true that what you say refer to PCIe slot.
It wasn't one of those cases where people connect to the pci port it the other way around and short circuit..
There is no visible damage to the GPU, to the little thingie going into the PCI slot of the MB or to the slot of the MB...
Ok, let's say it is no big deal!
Back to the point, so you decide to RMA your GPU? or a risers? I read all of the suggestion from the other member here, and
almost all deserve to be try. As long as you didn't do physical change, the warranty will be still valid.