I did not invest any skill points in manipulation in my current playthrough. Then, some time after I got the Neuro-Amp implant, the manipulation skill (rank 1) got unlocked, without me having to invest a skill point [NB: I fon't know which quest unlocked the skill, since I only noticed it when the skill challenge progress bar was displayed on the screen and I looked up the skills page. Going by logics, it likely was 'Executive Level', since that quest explicitely tells you that you can use manipulation in dialogues in order to sway the opinions of the board members on Infinity Ltd. and the Neuro-Amp].
Soon after that quest, I entered the Unity. At this point, I had three NPCs successfully manipulated, out of five I would have needed to complete the skill challenge.
In NG+, the Neuro-Amp was gone (which is not surprising). Rank 1 of the Manipulation skill was still unlocked and the skill challenge was at three out of five NPCs successfully manipulated; apparently, nothing did change by going through the Unity.
However, while I still can manipulate NPCs in dialogues, successful manipulations no longer count for the skill challenge, so I'm permanantly stuck with the progress I made before entering the Unity.