FedoraObjectResource around line 264:
If the ingested file is AtomZip, there's a check that the MIMEType is XML-compatible - this won't usually be the case for AtomZip.
If the test fails, the stream is left as null, and a new blank object is created.
The logic should be changed so that if a binary ingest format has been specified, this check for XML mime type is skipped.
Work-around is to specifty the parameter ignoreMime=true
Can be tested using the web admin client - export an object in AtomZIP format, then try ingesting it; you'll get an NPE (as the ZIP file being read at this point isn't a zip file, it's the template FOXML file created due to the MIME check above resulting in a null inputstream and therefore a template FOXML file being created).