I think I get it. The two halves of the preset (FXA and FXB) are both controlled by the same pedal, and you want to control them separately
What you will have to do is look at the parameters and find which parameter is externally controlled then change it. In this case, it will be easier to change FXB. So, do the following:
1) [PARAMETER], then <EDIT FXB>, then (MASTERS).
2) You will see that SEND has a line under it. This tells you that this parameter is modulated, in this case by 'ext1", the pedal. Let us change this.
3) Press and hold SEND, until you see <MODULATE>. Then hit <MODULATE>. This will bring up the normal controller screen, showing "ext1" as the source. Turn the wheel to select another source.
4) Then hit PROGRAM to exit and save it.
That should be it. I would suggest that you use another ext as the new source, or "off" if you want no external control to FXB. See pages 40-46 in the UM for information on modulation and controllers.