When mapping keyswitches, I seek to place the new keyswitch just before the note sounds, and keep the keyswitches at a very short duration. If the part consists of eighth notes, I will use 16th note keyswitches, if playing 16th notes, 32nd note keyswitches, etc., but not longer than 16th notes. Keyswitches are placed on a separate staff for each part and then imported into an empty layer of the instrument part just before exporting the notation file into my sequencer.
In essence, as DG said, when going back to a previous spot, if you do not have a keyswitch at that spot, the VI will play the last selected patch until your next keyswitch. If one has to keep going back to a particular spot, one can always add an extra duplicate keyswitch at that point. Note that I use Finale and Sonar, not Cubase.
HTH