Observations:
Surface scratches are just cosmetic and won't affect performance.
You either did damage it or did not, so at this point just trudge on and complete the build to find out.
If you DID damage it it's highly likely it's associated with something not important: like one of the unused PCIe slots. Or maybe something that you can put an AIC in to replace: like Audio section or NIC.
You might also could repair the damage: that depends on location and your skills. A picture would help.
Lastly: you did the damage so you can't return it, warranty doesn't cover your actions. You're stuck with it so disabuse yourself of any notions otherwise.
EDIT: you'll know you cut through the trace if it doesn't work... but you could also see it if you have a magnifier or take a picture zoomed in macro mode. You'll see some bright copper where you scratched away the solder resist, and if the scratch cut the trace you'll see a small gap. If you're clever you can bridge that gap with solder. It gets more difficult if solder resist as been scratched away from surrounding traces.