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The error indicates that there are some broken entities in your software library. Please file an SR and support can help you with this issue.
BTW, in EM 12 release 2, we ignore such errors and allow you to complete the migration.
How do we migrate it? I am at Enterprise>Provisioning & Patching > Software Library
Firstly, you should bookmark the URL below. This is the EM documentation and source of all information you would commonly need.
For details on migration, check this section in the admin guide:
Thank you afulay. It worked!!!