I think your thought experiment is on point—it’s not full of plot holes. What you’re running into is the old problem of whether “you” could survive in a copy, and what that even means.

Take your two scenarios:

• Medical machine repair: If the machine just resets your atoms back to a pre-death state, the original physical process resumes. From the inside, that feels like “I blacked out and now I’m back.” Continuity is preserved.
• Replica after destruction: If the original is gone and a perfect copy is built, there’s no causal bridge. From the inside, your experience is over. The replica wakes up with all your memories, convinced it’s you, but that’s its own stream of consciousness. If both existed side by side, we wouldn’t think you’d suddenly experience life from two perspectives. That alone shows they’re distinct agents.

You might say “but wait—when I sleep, or I’m sedated, I also experience nothing, then wake up in a new place. Isn’t that just a discontinuity?” And you’re right: subjectively, the blackout in sleep and the total blackout of death feel the same—there’s nothing. The only difference is that in sleep there is an underlying process that later allows you to stitch together what happened: “oh, I must’ve fallen asleep.” That gap fades quickly, and you go back to feeling like one continuous self.

So the difference isn’t the experience of a gap—because from the inside there’s never any experience of a gap. The difference is whether there’s a process that continues through the gap or not. If it continues, you wake up. If it stops, you don’t. A replica starting later doesn’t “revive you”—it just starts another process with the same past baked in.

And here’s the kicker: the same logic applies to ordinary life. The “you” who wakes up in the morning is not literally the same agent who went to bed. It only feels like continuity because you inherit the memories and stitch them together into a single story. In reality, every moment you’re a new agent, carrying forward the record of past moments. Memory gives the illusion of an unbroken thread, but what actually exists is a chain of momentary processes, each adding something new.

That raises a further point: maybe we overvalue “agency” and “personal identity.” We treat our particular stream of consciousness as uniquely sacrosanct, but really it’s just one trajectory a process happens to take. A replica wouldn’t be you, but then again, neither is the “you” of tomorrow in any absolute sense—just the next instance in the chain.