We have two Nexus 7706 switches in our data center. Both are running 8.2(1).
This morning, I went to remove a specific VLAN from a port-profile. This port-profile is tied to several VPC port-channel interfaces (shared across both 7Ks), which are trunks to our ESX servers. The configuration is like so:
port-profile type port-channel ESX switchport switchport mode trunk switchport trunk native vlan 999 switchport trunk allowed vlan 130-132,134-158,164-170,174,177-178,181 switchport trunk allowed vlan add 183-184,190,321,401,552,652,1000 spanning-tree port type edge trunk speed 10000 duplex full description ESX Server state enabled
When I display the running config, it's shown in the two-line format, with the second line using the "add" command. Thus, nothing should be overriding any other command.
When I did the remove of a single VLAN ID, the second line somehow got removed from the config. So, the switch updated the port profile to remove VLAN 140, but it also removed the second line with all of those VLANs.
I've removed VLANs numerous times before from these port profiles and have never seen this happen.