Hi,
Would you please tell where did you link the GPO1 and GPO2?On the DOMAIN level ,right?
I would recommend you run the command :gpresult /h on the server and DC to see if any errors happened. If the GPO2 is winning, you can also see the result.
If the GPOs were applied correctly, i don't think it won't cause any serious impact.But from my side , i would remove the settings if i don't need it anymore.
Based on my experience, it is not recommended to set the same configuration on different GPOs, it will make the environment more complicated .And it will be difficult for troubleshooting if you have more and more GPOs.
Best Regards,