I mistakenly created a disk in a repository that uses the same friendly name as an existing disk that is in use by a virtual machine.
Can I safely remove the second disk with out OVM trying to delete the original disk as well?
Yes, you will be safe, bacause OVM uses the disk ID to identify the disk.
You can also use the little triangle just to the left of the virtual disk name. It will open a message saying if disk is in use by a Virtual machine.
Also, the GUI will not let you delete a disk which is in use.
If you want another way, you can "edit" the disk in the OVMM GUI, read its ID, cancel the edit, and go delete it from a root command shell on the VM server.