She doesn't feel it, the cut that they make into her neck to open her up and dig her out, replace her with someone new - something else.
But when she wakes up she feels the absence of control and it's not hard to work out what had happened. She had been running from the Seekers after all, though she was surprised that her fall hadn't killed her. Perhaps she shouldn't be.
The Souls claim to be saving humanity, not killing it.
Instead she's trapped, feeling herself come back to life inside her own body but she can't do anything about it.