It appears that lower-level descriptions are defaulting to the default publication status (set via Admin > Settings > Global).
I've added this ticket to a watch list so we can try to fix it for the 2.4 release - at this point we're finalizing the packaging for 2.3 so unfortunately it won't make it in. The good news at least is that in 2.3, publication status has been moved to the job scheduler, so you can publish large descriptive hierarchies asynchronously without the operation timing out in the browser. It's not a fix obviously but at least there's a way to reliably resolve it after import. The other workaround would be to temporarily change the default publication status prior to import, and then change it back after. In 2.3, you'll now find the option to update publication status under the More button menu, rather than in the edit template.
RE: the reference code - yes, it sounds like this is caused by the repository inheritance setting. I'm assuming that parent identifiers were manually included at lower levels (e.g. assuming there are no intermediate levels, the file-level identifier is 001-1-1-1), so you're getting the "001" from both the child record and inherited from the parent.
Cheers,
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