The proper PS4 setup is not to have any individual config file contain the USB mode setting. The Quadstick should boot up in that mode and stay in it. The Titan Two flag must be off for directly connecting to the PS4. We only want that flag on when using a USB adapter between the Quadstick and the Console since the adapter is handling the authentication function.

Here is a video proper startup light sequence for the PS4/DS4:
https://www.youtube.com/watch?v=9HBt3EycuuI The green light should go through that blinking pattern with a 30 second pause after about 15 blinks the whole time.
These
setup instructions for the DS4 may need to be repeated. Playstation has a habit of forcing settings back to the defaults during system updates. Plugging the DS4 back in to the PS4 for charging may reestablish the Bluetooth connection and if that wakes up, the authentication will fail.
The timing of when things stop working can be helpful to know. 7.5 minutes, authentication failure. More than 10 minutes, power saving settings probably shut off the idle controller.
A
Brook Wingman XE/XE2 can be used in leu of a DS4 in the USB-A socket and it will not have any battery charge, timeout or Bluetooth connection complications.