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Stripping notes out is certainly straightforward, though irreversible ...

Code:
-- CAUTION !! DESTROYS NOTES PERMANENTLY …
tell application id "OGfl" to tell canvas of front window to set notes of graphics to ""
There is, however, a bit of a land-mine to avoid if you start to experiment with using script to strip out User Data key/value pairs.

NEVER RUN THIS:
(on my system it proves fatally data-destroying ...)
Code:
-- CAUTION !! DESTROYS WHOLE DOCUMENTS PERMANENTLY … (RENDERS THEM UNSAVEABLE, FOR SOME REASON …)
-- OS X 10.7 OmniGraffle/5.4/beta2-139.3
tell application id "OGfl" to tell canvas of front window to set user data of graphics to {name:""}