Innit. I’ve no idea (neither does the HR Partner know) how to resolve it really.
Simple. You’ve called him on his timekeeping with, I presume, evidence that his timekeeping is poor. He’s played the victim card which is BS, and called your bluff. It’s now up to you to continue with whatever course of action comes next, be it written warning or whatever. He’s taking the piss, you’ve called him on it and now he’s taking the piss again. It’s HR’s job to support you, not roll over and let him dictate how you handle him .
Yeah, I know my organisation was extremely hierarchical and disciplined, but what the hell is the point of a) a process and b) an HR dept/person if the colleague can defeat the process simply by pretending to be upset?
In all of that you’ll need a paper trail of your offers to support him throughout whatever is causing him to be late, plus a record of any verbal warnings you’ve given. If you haven’t already been through that process, bite the bullet and start again.