Hiya Tony
I'm assuming your reference to HD means that your KN6000 has a hard disk installed.
I had always understood that loading the next set of registrations - say 8 panel memories - from hard disk on the KN6000 was a very fast process say 2 - 3 seconds...and I think that is the way forward for you rather than tucking panel memory settings behind the midi file in the same saved file on your hard disk. Give that a try..in other words separate out the midi file from the next set of panel memory registrations on your hard disk.
As a matter of interest that's why I bought the KN7000 because the loading speed from the SD Card is phenominally fast.
Rog