Ambertape, I think that if you downloaded to 'My books' at home then you shouldn't expect to see the download at 'My books' at work. These are two entirely separate locations.
If both your home computer and your office computer are registered with Sony, then there should be no problem in re-downloading the books from Sony onto your work computer.
(I must admit that, in the interests of simplicity, I only have my home computer registered with Sony. I have a look at what's available at work, on the web, then download at home later. Your case illustrates the problems in having multiple iterations of the same thing. This can be managed if one knows what one is doing, but I am naturally cautious/stupid--take your pick.)
As for having both the connect software and the ebook library software on the same computer: I would be tempted to delete the older connect version in the interests of simplicity. The books should remain in 'My Books' and can be re-imported into the updated ebook library as described in my last post. (Or they can be re-downloaded from Sony. A prudent person might well save them elsewhere on the computer, just in case.) But if you are feeling particularly cautious then just leave the older Connect software undisturbed and use the new ebook library from now on.
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