Rei I, Rei II and Rei III Are Not Simple Save Files
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The series shows more than one Rei body and makes clear that replacement is possible, but it does not present each Rei as an identical continuation with nothing lost.
Rei II's death and Rei III's emotional discontinuity make that impossible to ignore.
Why it matters
The question is not only how
NERV can replace Rei's body. It is what memory, soul and personal experience mean when a body can be replaced but a relationship cannot simply be restored.
Rei II Chooses Shinji Over Gendo
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Rei begins the series defined by obedience and by a bond with Gendo that Shinji does not understand.
Across the middle of the series, her relationship with Shinji becomes increasingly personal. By the time
Armisael attacks, her willingness to destroy herself to protect him is not the behavior of a disposable tool.
What changed
Rei's choices begin to come from relationships she formed herself rather than from the role
NERV assigned her.
The Replacement Rei Exposes Gendo's Blind Spot
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After
Rei II dies, Rei III returns in a familiar body but does not reproduce the exact emotional relationship Gendo expects.
Gendo has built an entire plan around the assumption that Rei can remain a controllable vessel.
Why it matters
The replacement system can reproduce a body. It cannot guarantee the same person will keep making the same choices.
Rei and Kaworu Mirror Each Other Without Being the Same Thing
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Both Rei and
Kaworu appear human while being connected to beings outside ordinary humanity. Both are placed near Shinji by larger systems, and both eventually make choices that exceed the roles those systems assigned them.
Why it matters
Their similarity is thematic before it is encyclopedic. Evangelion uses both characters to ask whether origin determines identity.