From your own user handle, I assume that this subordinate works as a software developer.
I feel like I have to walk on eggshells, as part of the reasonable adjustments put in place already I can't Skype my subordinate when he works from home, I have to e-mail him, but he then ignores his e-mails. So I have no idea what he is doing or why his work is taking so long.
Having sat with him before his health conditions were disclosed to me, I found he was not able to focus on what he was doing and that he often sat staring at his screen for long durations of time doing nothing.
A software developer, who is not able to focus on his work and who stares at his screen all day, doesn't need less structure, he needs MORE structure.
In other words, he needs shorter feedback loops, and things like daily stand-ups, less social isolation, more face-to-face meetings, more pair programming opportunities, code reviews (not just his code review, everyone's code), screen-sharing turned on automatically when he's working remotely (like oDesk does, now called Upwork), etc.
Now, I am not a lawyer, nor do I work in HR. So take everything I say with a grain of salt. And nor do I know what that health condition is, and nor do I know what HR is trying to protect the company from by preventing you from skyping him.
But in my personal opinion, there are two possible options here:
HR is doing this worker a disservice by removing the little structure he does have.
You don't know how to give him structure without criticizing him and therefore HR is protecting him from you.
And hopefully, it's just you who doesn't know how to give him structure without criticizing him, because if it's you, that problem can probably be addressed. However, if it's just HR being incompetent, or the law not being conducive to solving these type of issues, then I don't know what to tell you about that.