I'm having this exact same issue as of 3 days ago. Completely stock PS4 Pro (original factory hard drive). The system worked perfectly up until this started happening. Now without fail, every time I put the system into rest mode the system will not wake back up when I attempt to turn it back on. When I power on the system from rest mode I'll get a pulsing yellow power bar light, the hard drive will spin up, and then it just sits there. I can get the system to boot by holding in the power button for several seconds, which causes the system to restart, do a system storage check, and then everything works. If I power the system off completely when I shut it down (not rest mode), it starts up fine the next time I turn it on.
This is aggravating and has to be related to a system or software update we received in the past week. I'm at work right now, so I can't tinker with the HDMI link stuff. Please let me know what people discover.