From what I have experienced, the pressure to go back to the way it used to be can be quite strong while implementing Holacracy, especially at the very beginning. Former bosses having a hard time letting go and accepting that others can probably do things just as well will unconsciously try to meddle in the way they used to (I know, because I'm one of them , trying my best to tone it down)
People seeking approval from their former bosses for decisions that their roles already have the authority to make, or asking the bosses to step in and make the decision for them are also quite common in my experience.
If this is the scenario you are describing, then my view is that it should be discouraged as much as possible. The reason why we are implementing Holacracy is to go towards distributed authority. If we wanted to stick with bosses overriding decisions and people seeking approval form their bosses then why implement Holacracy?
Having said that, it's really tough to convert over night, at least it has been the case for me, so we made some adjustments:
1. For things that I really couldn't let go yet, I proposed roles with the relevant domains and accountabilities in governance, and appoint myself to fill them.
2. We implemented the advice process: "When in doubt, ask the experts, and those that will be affected by the decision". Note that this is not approval, as the final say still rests with the role itself. This advice process is merely information and input seeking to get a more complete view before deciding. The decision can be completely against the recommendation of their former boss.
For your case, perhaps the same thing can be done. Let the CTO define what it is he still wants to have control of, and ask him to create the roles with the appropriate domains and accountabilities for it. As the CTO is also the Lead Link, he then appoints himself to those roles. Everything else then gets differentiated to other roles.
You may also want to further implement some kind of advice process so that the CTO and other experts are consulted, if applicable, when one or more roles want to make decisions. Be sure to explain that the final say is still with the roles, and that they should use their best judgement to decide what is best from all the inputs they get.
Hopefully this helps a little..
PS: By they way, where are you located, if you don't mind me asking ?