Had the same problem when I went to .588 and .595. Purchased apps show up but free ones do not. You can go to the web portal and download them manually (they are all still listed there) but I read many suggestions of clearing cache, etc. and none of it work.
I then installed ZombieStomped 1.7 and most of them came back! Don't know how or why, but they all re-synced when I did that.