apps in itunes but not on iphone sync screen

[tikigod19]

Hi guys, had a total nightmare with everything technical in my house this christmas. I had to format my pc and although I backed up my itunes library itl, I can not get my apps from itunes onto my phone. They are in the apps window on the left of itunes but when i go through syncing preferences with the iphone connected, the apps box is blank. Im worried that if i sync they will all be removed (indeed I started to sync and it said removing facebook...) when I cancelled the sync and checked the phone, it had gone.
Do I have to manually download them all again or something?!
Thanks

edit: after a couple of hours and a combination of right mouse button on the phone and selecting transfer purchases, and double clicking the app icons within itunes and locating manually seems to have sorted it.