So my theory is that Helena setup Petey reintegration in order to get Petey out of the picture.

I think Helena, in an attempt to win her father’s respect/attention/affection/etc tried to be fully involved with “Project Mark”. However Jame refused and Helena was sidelined. I think Helena then setup Petey finding a way to reintegrate, knowing it would get him kicked off the project. Once Petey was off the project Helena would volunteer for Severance to replace Petey, both putting her on the the biggest project they had and furthering the severance procedure.

As a result I think Helena is aware of reintegrate and could reintegrate, but given it’s current death track record, isn’t likely to do so, yet.

I suspect she knows where the doctor is and will attempt it in a future season, but hasn’t yet.