Hi there,
I've done it before on few occassions and there's no negative impact to VMs. What you need to do once you've associated datastores with that single storage profile, you need to go to properties-'General' tab of every VM and change Storage Profile entry to reflect the new one. It can be done while VM is running. If you don't do it, any changes to vApp/VM will error out due to incorrect storage profile associated with them (resulting error messages are often misleading or to generic). Once you've corrected storage profiles associations on all VMs, you'll then be able to delete *Any profile from vCD configuration (after associating default SP with another profile)
PeterD