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I will answer my question. I killed the migrating Java process and the migrating wizard will report failure of migrating the .jpr file. Actually, the only thing missing in the migrated .jpr file is deployment profile which I can generate from deployment menu. And I can deploy the migrated process. This works as a workaround.
We had the same problem. After talking to someone from Oracle we heard the problem might be related to the combination of JDeveloper 126.96.36.199 and the Sun JDK 6. We switched back to JDeveloper 188.8.131.52 (for migration only) and that solved our problem. JRockit might also solve it, however we did not test it.