Pretty sure they pull all the cyber, since they are trying to rebuild you as a base human and the cyber would get your machine-kill-fleshies thing happening.
Lessee...page 74-75
With registration, C-Swat pulls you in and tags your gear. You get monitoring and analysis until your orginal EMP is restored, ( unclear if this is your starting EMP or, more likely, the EMP you had until that last little bit that got the Squad after you...)
With therapy from a heavy metal psychiatrist, 2 whole POINTS of Empathy are brought back per week, but not until your cyber -a ll your cyber - is deactivated and/or pulled. Once that stuff is shut down and/or out you can start healing. There is no mention of putting it back in and for good reason - it would undo the therapy and let you get an endless amount of cyberware.
So there appears to be 2 kinds of treatment - a lesser one where you get weekly analysis and regain 2 HC per week until original EMP is restored, your cyber active but monitored, and the more extreme version where they have to forcibly jack you into therapy and pull all your gear. In that one, your gear doesn't come back. Until you re-buy it...while Max-Tac watches you like a hawk.