Hi Roger,just been looking at your problem, in my days in retail customer support with Yamaha and Technics products the problems with midi and interface connections was quite common.I have looked at the organ app.and the specs of the KN7 I have a few questions to see if I can figure out what is needed.
1-what type of interface connection are you using?(midi to usb adapter-ipad connector)??
2-How are you connecting the audio output of the ipad?
3-have you made a complete back-up of the KN7 settings so you have a safety net when you start experimenting with the KN's complex midi patches.(give me the good old days of 1 channel at a time)
The first thing to do is after a full back-up of the KN go into the control panel and initial the midi settings,or use the reset disc to reset the midi to factory settings.Next set the R1 output to ch 1,then test to see if you get any sounds??
If the app is set to default general organ channels (the older standards)upper manual ch1,lower manual to ch2, and pedals to ch3 you may have to reset these to upper ch1,lower ch3 so as to match the initial settings of the KN which is R1 ch1,R2 ch2 and left(lower) ch3.
Hope this helps,let me now how you get on? .There may be a way to do this all via USB. both midi and audio but still looking at this option.

Regards John.