The only correct, intended, non-hack ways to get a reference to an existing clone VI is to use the "This VI Reference" node on the clone VI's own block diagram and have the clone send that reference to someone else as part of its own execution.
Any other mechanism was never intended to work and is generally unstable outside of very specific use patterns.
There is one mechanism available, and I requested that R&D leave it working even though it can be unstable, and that is the Open VI Reference node when you pass a string. You can pass the qualified name of the original VI followed by a colon followed by an integer to get a reference to that specific clone. The big big big caveat is that you need to close that reference before the clone is disposed. This technique is used by the LV Task Manager, and that tool is the only reason that this feature remains instead of being fixed as a bug. Unfortunately, it really isn't possible to make this feature stable without a significant performance hit on calls to clone VIs. It wasn't intended to work, which is why there's no official way to do it, just the devs forgot to close Open VI Reference loophole.
Even if you do get a reference to one clone, any properties you set on that clone while running will be set only on that clone. Likewise, anything you set on the original VI ref will only be set on the original VI (with exception of breakpoints). LV has intentionally never created a "me and all my clones" ref (the reasons why are a topic for a different discussion thread).
If you make changes to the original VI BEFORE the clones are replicated, then the clones will have any changes you make. That generally means never calling the original VI as a subVI and instead always calling it through Call By Reference node.