You should be able to transfer them to Calibre from iBooks. However, the Apple DRM will prevent you from being able to read them.
If in iBooks connect to PC/Mac and open iTunes. Select the iPad in the devices list in left side bar if visible. Select apps tab and scroll down until you find iBooks and select. A list of all the books will be visible in iTunes. Select and drag them to the calibre window.
For other reader apps visible in iTunes, do the same.
Once they are in Calibre add new books to Calibre and it will upload them to the iPad.
There is a Calibre thread for more specific info.
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