The archive feature is offered by Amazon for books you've purchased from Amazon. So, unless I'm misunderstanding the question, no, you cannot archive books you didn't buy from Amazon.
I'm not sure about ebooks you email to Amazon...I thought they didn't show up in the archives past a very brief window of time allowing you to download them to your assorted kindles.
From the Kindle Help pages:
Removing Personal Content
Personal documents you transfer to your Kindle are not backed up at Amazon.com. If you wish to keep a copy of personal items for backup before deleting them from your Kindle, you'll need to save them to your computer or another storage device.
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