If I have two (switch1 and switch2) cisco 5xxx switches trunked using dot1q. Switch1 is in server mode with domain name Frank and Switch2 is also in server mode with doman name Sandy. Will their vlans get mixed up?
I would just run the switches in transparent mode and manually prune off any vlans you don't want talking between the switches . To be safe I would not have duplicate vlans on each switch like vlan 2 on each side if you don't want them talking .
Current best practice is what vipergg says. Use vtp transparent mode but prune by only allowing the vlans you want carried on trunks. Think seriously about moving to L3 and removing L2 if $$ allows.
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