Unfortunately, I missed the message and I lost the apps. Fortunately most of them were free, so I just reloaded.
When you have to sync with iTunes, I find it a little cumbersome. You need to remember that if you want to sync Photos, and you are in the Photos section, When you click on that sync button. Its syncs with everything else music, film, apps etc.
So the lesson here for me was, even though I am doing one task, and that was syncing photos. You need to check the other sections to make sure that you are not going to alter that status as well. Most importantly, make sure your apps are saved.
I don't like the idea that I can only transfer a folder and not just a few photos.