>>3869473>that was never actually explained or hinted atI think it was hinted at in Q and perhaps explained in 3+1.
The method we saw in the TV series did not get the correct results. Rei goes off to do her own thing. They can't get a different girl to use so they have to remove/keep trapped the independent parts of Rei's soul.
Rei Q was an obedient part that is supposed to trigger an Impact the way the manipulators want it done.
Considering how little the TV series explained anything (dummyplugs, the Lance, even LCL which was presented with a few facts but nothing beyond that) and the complete assault of EoE, it is not surprising Rebuild would make up rules as it goes along.