you can configure only 1 single native vlan per a single trunk link. Latest native vlan x command will override previous native vlan Y command. So, it's not possible to have multiple native vlans on a single trunk link. But You can have different native vlans on different links between switches; they must match on the same single trunk link between sw A and sw B. Traffic in those native vlans will be blocked.
Note that you can configure switch A native vlan X and switch B in native vlan B and trunk will work for other vlans. Switches will complain that you have so called " native vlans mismatch" on a single p2p trunk. Here, in this case, traffic in vlan A and B will not be OK but all Other Traffic in other vlans will be OK.
So, You can have different native vlans on different links between switches. i.e. swtich A to B natvie vlan X and sw A to sw C has native vlan Y will be ok. Depends on vlan configs, some traffic will be ok; show interface trunk and show spanning vlan x
Regards, ML **Please Rate All Helpful Responses **