Go ahead and delete one of them. You can easily rename VM's or even recreate deleted VM's. After all, A VM is just a bunch of settings (except when it contains a virtual hard drive - read on...). Verify that the remaining VM points to your Boot Camp partition or just make it point to your Boot Camp partition.
When you remove a VM from the Virtual Machines List, Parallels gives you the option of keeping it or moving it to the trash. If the VM contains a virtual hard disk that you want to keep, then you can go into the VM (right click in the Finder and Show Package Contents) and move the .hdd out of the VM before emptying the trash. Note you don't need to keep .hdd's that point to Boot Camp partitions since they can be recreated when you create a VM.
