I struggled to grasp that as well, at first. Without wearing a device, how exactly did she get into a Peripheral? This article suggests that the Flynne that gets shot isn't "occupied", so to speak, but is rather being driven remotely by Flynne from the new stub she created as if it was itself a Peripheral. It requires some assumptions, and although I suppose its plausible, I'm not sure the show itself supports it.
https://www.cnet.com/culture/entertainment/the-peripheral-that-ending-and-post-credits-scene-explained/
That end stitch is where things become Westworld-level tricky. Because of the show's editing, it looks like the consciousness of the dead Flynne has been transferred to Flynne's peripheral (the future robot body accessed via the special headset). However, the past Flynne died without wearing a headset. The way this is possible might be that, because Flynne created a new base stub, she was only a pilot in her old body. When it died, she returned to her new stub, then from there, still wearing the headset, she could jump into her future peripheral. Good luck deciphering all that!
The other option I can think of entails an even greater sacrifice. The new "stub" creates a "copy" of herself, with all her knowledge at that point in time (the moment she created the new offshoot). So, she truly has herself killed knowing that her other version is an exact copy. In this way it’s somewhat akin to the excellent "The Prestige", where Angier kills himself when using Tesla's failed teleportation machine (that really just splits him into two identical versions) knowing a new "copy" will be created (since both versions are literally him).
That’s my preferred explanation, anyway, given what we were shown. She copies everything, including herself, trusting the new version of herself will pick up where she left off, then has her old "prestige" killed to protect her "original" stub and everyone else in it.
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Never believe. Always question. Rebuke belief, a.k.a. bias, a.k.a. groupthink, a.k.a. ideology, the bane of skeptical, logical reason.
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