download your books with ade from the kobo site and put them on the kobo through calibre.
easiest and pain free way to work around all of the problems.
having the books on the kobo app on the phone is nice but there are plenty of readers available for android and iphones. i use fbreader, and just send an epub to my phone that i'm currently reading so if i don't have my kobo with me i read a bit on my phone. i also send it to my office and have a copy of the epub at home and use those on my pc through the firefox epub plugin. this way whatever current book i'm reading i have access to where ever i am. when i'm done i delete all of the instances and just have the 1 left on my kobo. all that extra stuff i mentioned probably wasn't necessary but i wanted to mention it lol. the top part is relevant to your problems.