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Do you ever have the files open on more than one computer at a time while making changes? Doing so can produce unexpected results, though I'm not sure I can explain yours, especially not knowing how it originally looked.

You might consider using Help->Send Feedback to send in a copy of your damaged file to Omni; perhaps there are some clues to be found within it. There's an option to change the text to gibberish if the contents are confidential.