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You should be able to use Calibre's "connect to folder" functionality too connect to your device's SD card (either removed from the device and connected to the PC, or via the device plugged in through USB). If you do that, you have to put the books in the ebooks/import folder off of the sdcard root (create that path if it doesn't exist). Then you can use Aldiko's Import menu item to scan that folder on the SD card and load them into its library. It's not ideal, but it works.
Alternatively, I believe Aldiko supports OPDS feeds such as the one provided by Calibre's content server. Rather than syncing books through USB or SD card, just download them over your network. Books are small and the transfer is quick.
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