This isn't a particularly good answer, as I haven't had the chance to open a DS4 yet, but I can almost guarantee that something fell out or was misplaced when you replaced your joysticks, typically a lot of components are sitting loose in the enclosure, especially face buttons. If you don't get an answer that's a bit more helpful, try opening the controller in question as well as another controller that hasn't been opened, see if there's any discrepancies. Just make sure to keep the front of the controller facing down so none of the buttons or anything fall out, I think that's mentioned in the joystick replacement guide as well.
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