Github user alopresto commented on the issue:

    https://github.com/apache/nifi/pull/1261
  
    @YolandaMDavis caught a tricky one. When performing the migration of 
`flow.xml.gz` with an already-encrypted `nifi.properties` but using the 
`-x`/`--encryptFlowXmlOnly` flag, the new `nifi.sensitive.props.key` value is 
manually encrypted and updated in the `NiFiProperties` object before being 
re-serialized to the file. However, because this was not going through the 
normal "encrypt the entire object" logic, the protection scheme in 
`nifi.sensitive.props.key.protected` was being erased. This resulted in cipher 
text being stored as the key without an indicator of how to decrypt it. 
    
    I added an assertion in the test covering this scenario and was able to 
reproduce immediately. I applied the fix and pushed. Thanks Yolanda. 


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