Outlook 2013, auto-archive appeared to archive from one open archive file to another

Outlook 2013's auto-archive function appears to have archived some of the items out of one archive file into another, and simply deleted other items out of the first archive file. How do I tell auto-archive to not do this?

Last week I reorganized my archived emails into 3 pst files:
In outlook, I set the auto- archive file to archive-3.pst and updated my mailbox's folders (Inbox, Deleted items and Sent items) to use the default.

This morning, outlook's auto-archive function kicked off. The archive files archive-2.pst and archive-3.pst were open in outlook when auto-archive kicked off. The archive-3.pst file became much larger (from 200k to ~2GB) than I expected. Almost all of the items that were in archive-2.pst (~6GB) are gone. So it appears that the auto-archive function archived some mail from archivefile2 into archivefile3, and deleted other mail from archivefile2.

To put it mildly, this is not what I wanted. Why did auto-archive do this?
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MikeBroderickAuthor Commented:
I found the problem. Somehow some of the folders within the Archive file were set to the default archive settings instead of "do not archive". When I changed them to "do not archive", it worked.

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