I can't find anything specifically about taking a VM from one vApp and cloning it directly into a new vApp. You may need to take that VM, create a new vApp template with it, then deploy that VM from the template. Would be more straightforward if you already have a Template with the VM you need in it, but if you don't you could create it.
Would have to whip up a script to do that using these cmdlets:
Get-CIVMTemplate, New-CIVM, New-CIvAppTemplate
I know its not exactly what you're looking for, but with some juggling you could make it work.