Hi Dallas,
Are both Delphix engines the same version? Are you using the same operating system user for discovery? Were any hotfixes applied to one engine but not the other?
It sounds like discovery is failing. I think we would probably have to look at the debug logs to see why discovery failed to find the environment.
I've only tested adding the same environment to two different engines for databases (Oracle, MSSQL and ASE). Are you doing this for unstructured files or EBS?