This is where my lack of knowledge becomes (even more) apparent--ADE seems to consider the last book (by date and time I think) loaded sorta kinda primary in terms of what ADE account will work at any given time. If you have an SD card of books bought in, say, September and you have an October book on your Kobo, then the SD account books may be locked out until later books are no longer there.
Test it and see! You won't harm your Kobo reader and you will advance the knowledge of Kobo users all over the world.