Hi Rasmus,
When configuring replication you choose the target datastore location for the replica files.
vSphere Replication will warn you, if you by mistake select the datastore folder of the source VM disks.
The recover operation always registers a new VM. You need to select a VM & templates folder in vCenter Server that does not have VM with the same name.
Be careful if/when removing the original source VM - vSphere Replication automatically cleans up any replica files, when the source VM is removed from the source vCenter Server inventory, unless recovery has been successfully performed on the replication.
Regards,
Martin