Comentário oficial
Sorry, there's no way to force-override the internal FX, and to be honest, the internal effects are better because they're not only beat-linked, but there are a heck of a lot more of them with additional parameters available.
There may be a mis-match between the hardware control and the software knob position if you have switched the FX to an analog input changed the level knob, then back to a rekordbox channel -- the hardware and software are in different positions and won't match, so you need to move the hardware to "pick up" the software.