I think Koert is on the right track - it looks as though the elements in the file probably have DataGroup instance data that is older (or in some way different) than what exists at the system level. For example, if you place a few doors in a file, exit, go and add a new property to the door schema, and then reopen that DGN file, the existing doors will have a missing property - the DataGroup Update utility resynchronizes the instance data to the system data.
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