I did a post about the multile shelves a few months back, it drives me nuts too. I was told it would fix in the next firmware.... I skimmed all the posts and saw someone mentioned the Kobo Server. If that's the issue my teensy it of it is still broken.
My books with the 'tap to download' do disappear from my iPad when I put them in Trash on the kobo website. I sync my KT later to see if they have gone from there for sure for you.
It makes me fed up too.