Let's take this scenario. You have LUN1 with 2 VMs, vm1 and vm2. You perform a SRM Test and take a clone of LUN1. Once the clone is finished you cancel the SRM Test. At that point you take the clone and present it to the DR ESX servers. You perform a disk rescan in vCenter and you see the clone LUN. At that point you browse the datastore of the clone and locate vm1. Right-click on the vmx file and select "Add to Inventory." Name the VM whatever you want, just don't name it the same name that SRM is using (i.e. vm1). For example, name it vm1-clone. Do the same for vm2, vm2-clone.
The above steps should work just fine and it will not cause any issue with SRM. You don't have to reconfigure SRM. Once you are all done with the clone remove the VM from inventory.