Unless the books are DRM (Digital Rights Management) free, then the only way you'll be able to download and use them again is through Sony's site and apps. But you might be able to work around retrieving the files in a couple of ways.
I understand Sony has Kobo software for your computer as well. If you can use that to find and download the books, then find the files, you 'might' be able to use File Sharing through iTunes to side load the books into the Kobo app.
http://support.apple.com/en-us/HT201301
{this support pages is an older version of iTunes. The buttons and places have changed, but in principle its the same. I couldn't find a more recent version.}
There are a couple of computer apps that will let you browse your iPad's file directory, to some extent. The iPad's file structure wasn't meant to be directly accessible to users, so it's not organized in anything like a friendly way; but if you can find the files you can download them to the computer. The same apps will sometimes let you put files on the iPad.
The only one that comes to mind is iFunBox. I'm pretty sure there are two or three others.
If File Sharing through iTunes works for the Kobo app, it's safer. But nothing is guaranteed to work. Besides moving the books you're all also needs to be registered so that it can unlock the DRM. I have no idea how the Kobo app does this.
I have no way of testing either of these solutions.
If the books are not overly expensive, and you only have 2, then it might just be cheaper, and certainly less trouble, to buy them again on the Kindle or iBooks platform. Such is the painful reality of DRM.
