Motherboard PCI E Slot

I think I might've damaged the PCI E slot on my motherboard when taking out an old GPU. I RMA'd the GPU just to be safe but I still have my worries. When I get my card back, and pop it into the uppermost PCI E slot, and no data is sent to the motherboard, can I use my bottom slot? I know that the bottom slot runs at 8x speeds, so how much would that bottleneck my gaming perfomance if I am able to use the bottom slot? I am using an FX 4100 and a motherboard without display out. I can't test to see if my PCI E slot is broken right now because I don't have a spare GPU. Any help would be appreciated.

Which generation of PCIe is it, which GPU were you using and also yes you can use the bottom slot only it might bottleneck your GPU.

what gpu is it?

650ti

PCI E 2.0, and a 650ti

I think you might be in luck, assuming you have one monitor at 1080p or something it shouldn't be a bottleneck, if you are running multiple monitors though or a huge res then it might be a bottleneck.