I'd could see why the OS may reconnect and appear available while Pro Tools wouldn't without a relaunch. But it doesn't explain why relaunching the app won't see anything but the aggregate I/O.
Points to something else, and yes, I'm suspecting the OWC Thunderbolt 3 dock as everything was running through it. Not sure exactly how to test for it though, to be sure.
Usual playback engines seen are:
PT Playback Normal.jpg
Relaunching after the problem presents produces this:
PT Playback on Relaunch.jpg
Now, if it's the dock, I get why both the interface and the dock might not show upon relaunch. I can't explain the rest missing as they're software/system options. But there you go.
I've been a little suspicious of the Thunderbolt dock after replacing my Mbox 3 Mini with the Clarett, which requires an external power source. Switching the Clarett on, the light on my iLock dongle plugged in the dock would often go out.