Hi Gary, yes, iCloud (or maybe Dropbox, depending on what the APIs look like) is in the works in the next few months. VERY sorry to hear about the loss of data. The time put into layouts is incalculable, particularly because it happens over weeks, months and years. The restore process should restore your MIDI Designer data if you backed up the apps as well.
Anyway, so sorry to hear about your loss again, and yes, some kind of automatic backup that goes beyond your device (meaning to the Cloud, somehow) is coming soon.
On the silver-lining side, perhaps redoing the layouts will enable you to refactor better, somehow. However, we feel your pain. Everybody who works with a computer has lost huge amounts of data at some point (and we have, personally, at several points)... we hope your'e not discouraged from putting some MD layouts together for your use.
Good luck and thanks for the suggestion. This is part of the why-doesn't-this-app-have-this-basic thing list that is part of any indie app.