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What happens if you use iTunes to directly deposit the file in OmniGraffle on the iPad? Cable up the iPad to the Mac, launch iTunes, select the iPad in the devices list, select Apps, scroll to the bottom of the page, select OmniGraffle in the list of apps supporting File Sharing, then click the Add... button and select your document. After it has copied the document to the iPad, launch OmniGraffle on the iPad and see how it reacts. Does it draw a preview for the document? Will it open the document?

It would be interesting to know if you can get the file to load if you delete most of the objects (try this on a copy, obviously!), which might suggest a memory limitation of some sort. Which versions of the apps are you using? Are you able to make a new document on the iPad, send it to the Mac, make some changes, and get it to load on the iPad? If you can't get it to work at all, that's probably a different sort of problem.

If you use Help->Send Feedback in OmniGraffle on the Mac, there's an option to convert all text in the document to gibberish to protect confidential information (assuming that the confidential information is textual, of course).

If you haven't gotten it working by Tuesday, you should call up the Omni support folks and get their assistance. 800-315-6664 or +1-206-523-4152 during normal business hours in Seattle. Posting here is not the same as contacting them...