To rename the VTP domain name you simply issue the following commands:
For IOS: vtp domain
For COS: set vtp domain
YES there are GOTCHAS!!! When you rename a VTP domain on a switch, the configuration revision number is set to 0 so when it synchronizes with the "new" VTP domain, the existing Vlan database on the switch will be overwritten.
No. In transparent mode the configuration revision number will always be 0.
Usually in transparent mode a VTP domain name is not needed, but depending on the OS (IOS vs. COS) if you are using the switch to pass VTP information to servers or clients you will want to make sure the VTP name matches the clients and servers. Also if you are using the dynamic trunking protocol (auto or desirable modes) to form a trunk, you will want to make sure the VTP domain names match between switches.