I discovered something just now. As above we managed to export to xmi from a corrupt repository by skipping the java.lang.ClassCastException: org.eclipse.emf.cdo.common.revision.CDORevisionUtil$uninitialized

The resultant xmi file is Imported into a empty CDO repo and opened in a Text editor

We get this, clearly were the problem lies.

[code]
  <model:MappingSubstitution xmi:id="t40167" substitutionFields="NNULL" name="Mapping BBG COLLAT_TYPE to collateraltype">
    <uuid xmi:id="t40168" lsb="-6140311635292653201" msb="9063455697632575823"/>
   ...
  </model:MappingSubstitution>

[/code]

Note the NNULL

This is the equivalent input xmi element
[code]
  <edmmodel:MappingSubstitution name="Mapping BBG COLLAT_TYPE to collateraltype">
    <uuid lsb="-6140311635292653201" msb="9063455697632575823"/>
    <substitutionFields inputField="/936/@containedField.14" outputField="/1186/@containedField.0">
      <uuid lsb="-8198965334738203190" msb="-2815692950055403294"/>
    </substitutionFields>
...
  </edmmodel>
[/code]

This suggests the /936 offset to the related object of Class TransformationNodePort is incorrect?

No idea how to fix this though, a weakness of the offset notation used is you cannot easily find the reference objects, much better to use something like the href.