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Had the same problem myself. I don't know but it might have something to do with the fact that when Aldiko imports your own books it also copies them to its own folder, giving you twice the books and used space you started with.
As far as I can remember, I solved it by clearing all books out of Aldiko, deleting my own folder and then using just the folder that Aldiko insists on using to import from. It worked for me, your situation might be different though.
Cheers.
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