Are you exporting a large geographic area, a large amount of data, or both? I'm guessing you've tried this multiple times, is it always the same part of the dgn that is missing? I've previously run into problems with dgn to kmz translations with large geographic areas and/or a lot of data. The first thing I would try is to isolate the part of the dgn that doesn't display in a separate model and just export that.
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