Found a workaround to this problem finally, just posting here in case anyone else is having this issue.

I'm using Photoshop CC (18, then updated to 19 in the middle of this mess) with a Cintiq Companion and the last month has come with a new forced Windows update and driver updates from Wacom. Historically there's been an issue running various versions of Photoshop in conjunction with Windows Ink. With this last update, the issue is that the cursor went missing entirely. Untoggling Windows Ink from the Wacom Tablet Properties would remove all pressure sensitivity from the Cintiq pen, which is pointless, but toggling it would remove the cursor from Photoshop, making it extremely difficult to paint or select with accuracy. Normally the fix is to reinstall older versions of the Wacom drivers but this time, uninstalling and reinstalling 2 drivers back did not solve the issue for me.

Workaround: It's so stupid. Go into Settings > Devices > Pen & Windows Ink and toggle "Show Cursor". That's it. That's the fix. This cost me hours of productivity. Hope this helps someone else.