Only ePubs purchased and downloaded via Adobe Digital Edition appear within the "My Digital Editions" folder.
Kobo Desktop maintains it's own store of kepubs it has downloaded within the Appdata tree of your Windows account; mine is at C:\Users\Peter\AppData\Local\Kobo\Kobo Desktop Edition\kepub
These files are however encrypted by Kobo's own scheme, and are also named with UUID type names (in my case
Code:
Directory of C:\Users\Peter\AppData\Local\Kobo\Kobo Desktop Edition\kepu
25/08/2014 21:33 <DIR> .
25/08/2014 21:33 <DIR> ..
27/07/2014 19:15 732,913 0ee44cf7-e192-4f5c-a84a-f719e93eb038
15/08/2014 23:03 5,901,364 2a89c344-38d2-4968-a66c-64d9995787ee
15/08/2014 23:03 12,162,967 c4b99f83-944f-4ef4-a953-a7a758ffeead
)