As far as using just ADE to add books to your Kobo, if you do this there's the problem with the tiny fonts people have experienced.
When I first got mine I uploaded my purchased books (that I bought from Kobo) using ADE, but they all displayed in a tiny font that couldn't be made large. I emailed Kobo and they told me to sync my device with the desktop app, which fixed the problem.
I've only synced my Kobo once, so I haven't experienced what you have, but I can see how it'll be annoying and frustrating.
Did you email Kobo back asking why you had to delete them from your library and if they're making a fix for this? I don't want to delete books I've purchased either.