A true monist would realize that any experience of the uploaded being that received a copy of the brain is not felt by the original brain that has been copied. This is a fact and it is elementary to see it as true, as well as supporting the view that the copy is not the same being at all. If your description of computation functionalists is accurate, then they simply are dualists and would do good in admitting this to themselves.
Invoking the Ship of Theseus is a distraction. The Ship of Theseus paradox does not involve a full copy at the atomic level while the original still stands. If it did, the paradox would not even exists. The paradox exists because there is the key element that you do not have in mind copying/uploading: _continuity_.
Isn't continuity just an implementation detail? Suppose your brain was replaced a bit at a time with mechanical hardware, the end result is an uploaded mind while maintaining continuity.
Imagine you are destroyed in your sleep by aliens and replaced by an atomically identical duplicate. Would you call this "you"?
If not, what if the aliens recycled the atoms from your original body to make the new body, putting each original atom into the same original spot with the same position and momentum (ignoring quantum and uncertainty principle).
What if they recycled 99% of the atoms from your original body, but swapped 1% of them for different atoms?
What if they only destroyed 5% of your brain and reassembled that destroyed portion, leaving the rest of you untouched? What about 50%?
What if they waited 1 planck moment before reassembling you versus 5 seconds?
Where is your dividing line in this scenario space between "that's really me" versus "that's just a copy and is not really me" ?
The functionalist answer, as I understand it, is fungibility across time and copies when arriving at definitions of words like "you".
The functionalist answer is not that > 1 copy can communicate telepathically or supernaturally share experiences is a dualist sense. They are still causally independent physical entities.
There is no prove that continuity really matters. In fact who goes to say that your current conscious self is the same as your self from five minutes ago. After all you do not feel what they felt. The only thing that makes you think that the two are related or even the same is your state (memories, emotions). Why would we even think about whether cloning is able to transmit consciousness when we don’t even know if consciousness is transmitted over time?
Edit: Just to clarify my opinion: This means that the relationship between my self from five seconds ago and my current self and the relationship between my self from five seconds ago and a clone of that self that aged the same amount would be equivalent. Both of us would _not_ be the same as my past self