The snapshot and replica are actually independent of each other. While the replica is based on the snapshot you can still delete the snapshot from the VM without affecting the replica.
Also the replicas are protected in vCenter so that you can not accidently delete. Once you delete whatever clones are tied to that replica VMware View should delete the replica.
Not that I am aware of. There are a couple of threads about which replica is tied to which linked clones and some solutions. You may be able to use the composer View of a pool inventory to look at a particular VM and try to back track it that way.