Hi haidar,
Regardung: "Is it recommended to change this to a different Vlan on the VPC Peer-Link on our Nexus Cores, or do we just leave it as default Vlan 1?"
As you may know the best practice regarding not to use vlan 1 is for security purposes, in case of your core devices there is no harm on leave native in 1, but just on these ports all other trunks or access port should have a different untagged traffic vlan.
And for : "
On the VPC links to the server virtual environment, if we change Native Vlan to say 100, would there be an option on the server side to change this to Vlan 100 as well so that both end match and not get a mismatch? Or does this behavior happens between switches only"
If server side is running trunk you will have an option to change this, could be named as native vlan or untagged traffic/port vlan.
HTH,
AL