I have seen such thing, but it's more then 4 years back since I did my last conversion.
Check if there are some layers in your OA database which have either the layer name or the purpose "unknown".
I can't remmeber to what the layers have been assigned to, also I don't know if the "unkown" was in small or capital letters.
Best is to filter your shapes for the layer name or lpp throug SKILL.
If you find such a layer in the OA db check if the shape is the same as the layer your missing form CDB.