I now put each card in the secondary slot by their own. Check GPU-z with first card in, PCIe x2, did a render test, dident up the speed only changed it to 2.0 instead of 1.1. Put in the other card there and checked and it gave me PCIe x8. Now i've put bouth back in and it went back to the way it was, PCIe x2 and x8
I'll check for damage in the slots and then I'll reset BIOS, see what happens if nothing changes then I'll update BIOS. Thanks so far guys, atleast now I have something to follow. Its likely the slot is glitchy, because It did run in x8 as I said before when I tried the second card in the secondary slot. But yea, it changed back when I put in the other card.