At Evil Controllers we only use official stock controllers provided by Sony. These are the same controllers you would buy at your local department store, except with our modifications added to them. Our modifications actually have no effect on the component of your controller that syncs it to your console.
As a result, if your controller is having issues syncing to your console, we recommend you follow these steps. These steps are what is recommended on a very popular forum thread on Sony's official message board. (The original source will be linked at the bottom.)
1) First Try This:
1. Turn off your PS4. (Make sure controller is not plugged in)
2. Find a paperclip or something to reset controller. (Under the L2 button)
3. Hold reset button for ten seconds
4. Press and hold the Playstation button. It should turn your PS4 on
2) If that doesn't work, Sony has this guide for syncing blue tooth devices:
Players have used this method to restore their controller's connection.
3) If neither of those methods have worked, we recommend the following, based on feedback provided from PlayStation gamers that have had similar issues.
1. Turn on your PS4
2. Once your console is running. Unplug the console from it's power source. We recommend having your console connected to a surge protector and turning off the surge protector rather than pulling the cord from an outlet.
3. Once the console reboots it will rebuild it's system files. Once this is complete your controllers should now be synced or will be able to sync through the standard methods.
Here is the Official Sony PlayStation forum that people have used to post and identify these solutions: