I've been trying to troubleshoot this for the past couple of hours now and have gotten nowhere with this. I recently got an Intel X520-DA1 10GbE networking card to add to my computer. My motherboard (Asus TUF Gaming Z690-PLUS Wifi D4) has 2 PCIEx16 slots. I had my HBA card plugged into the bottom slot and I plugged my network card into the top slot. The lights on the back of the networking card lit up when I first plugged it in, but then I took it back out to reseat the card. After reseating the card, the lights no longer lit up. After booting into Unraid, I ran lspci and found that it was not detecting the networking card.
I removed the card and moved the HBA card up to the top slot to verify that the PCIE slot still works. The HBA card worked just fine in the top slot and when I plugged the networking card into the bottom slot, it again did not light up. I plugged the networking card into a free slot that I had in my gaming computer and it lit up without any issue.
It seems like my motherboard is disabling the second x16 slot when the other is in use, but I'm not sure why. I have 2 m.2 ssds installed as well.