Hmm. I think your GPU would run in 8x mode, but it should be fine, even sharing lanes with the network card.
I've run cards off mobos with the same number of lanes, and a very similar gigabyte pcie network card, and it ran flawlessly.
I'd check the physical connection, look for damage to the antenna connectors where the wire meets the SMA connector, and try swapping in the old GPU as a control if you still have it. On paper, things should still be fine.