Issues with migrating lookups from 9.0.3 to 9.2

Below is a text from a TAR we've submitted with Oracle. Has anyone else run into this issue when upgrading from 9.0.3 to 9.2?
Lookups conditions not being properly migrated is a known issue when upgrading from OWB 9.0.3 to 9.2,
documented in Bug 3989847 - Generated Code Has Invalid Aliases After Upgrade From 9.0.3 to 9.2

Did you try putting the toplinkProject.xml into the META-INF directory? Does the same error occur?

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    <?xml version="1.0" encoding="windows-1252" standalone="no"?>
    <log>
    <record>
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      <logger>oracle.dbtools.migration.workbench.core.MigrationLogResourceBundle</logger>
      <level>SEVERE</level>
      <class>oracle.dbtools.migration.workbench.core.logging.MigrationLogUtil</class>
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          <line>1078</line>
        </frame>
        <frame>
          <class>oracle.dbtools.migration.convert.ConverterWorker</class>
          <line>316</line>
        </frame>
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          <class>oracle.dbtools.migration.workbench.core.ui.FullMigrateTask</class>
          <line>1002</line>
        </frame>
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          <line>303</line>
        </frame>
        <frame>
          <class>oracle.dbtools.migration.workbench.core.ui.FullMigrateTask</class>
          <line>205</line>
        </frame>
        <frame>
          <class>oracle.dbtools.migration.workbench.core.ui.FullMigrateTask</class>
          <line>159</line>
        </frame>
        <frame>
          <class>oracle.dbtools.raptor.backgroundTask.RaptorTask</class>
          <line>193</line>
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          <line>441</line>
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          <line>303</line>
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          <line>138</line>
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          <class>java.util.concurrent.ThreadPoolExecutor$Worker</class>
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      <logger>oracle.dbtools.migration.workbench.core.MigrationLogResourceBundle</logger>
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          <line>205</line>
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    Kris

    Hi Wolfgang,
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      OBJTYPE VARCHAR2(40),
      OBJECTIDS OBJECTIDLIST,
      NAMES NAMELIST,
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    GRANTEE PRIVILEGE ADM
    PDM_MIGRATION ALTER SESSION NO
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    PDM_MIGRATION CREATE DATABASE LINK NO
    PDM_MIGRATION CREATE PROCEDURE NO
    PDM_MIGRATION CREATE SEQUENCE NO
    PDM_MIGRATION CREATE SESSION NO
    PDM_MIGRATION CREATE SYNONYM NO
    PDM_MIGRATION CREATE TABLE NO
    PDM_MIGRATION CREATE TRIGGER NO
    PDM_MIGRATION CREATE VIEW NO
    PDM_MIGRATION UNLIMITED TABLESPACE NO
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    GRANTEE GRANTED_ROLE ADM DEF
    PDM_MIGRATION CONNECT NO  YES
    PDM_MIGRATION RESOURCE NO  YES
    Best regards,
    Kris

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