The genetic alterations of Rachel's powers would still be there and the specific aspects that keep Rachel alive would still function normally. However, she wouldn't be able to access any of the added magical abilities that came with them unless she regained them via the points system as those parts would be zeroed upon arrival. The clause you referenced doesn't give a character's powers in such situations a complete pass, but only the specific parts that are necessary for survival and nothing else. It's similar to the situation with Force-using characters; they loose their connection to the Force on arrival, but the midi-chlorians that normally allow that connection aren't actually removed from their bodies.

Let us know if this answers your question, or if you have any further questions.