Gotten new replacement 3GS but iTunes will not sync data iPhone 3G

hi all! i have gotten a replacement phone for my 3GS as the battery was draining like crazy ever since i updated to OS4.3.
so when i tried to sync my apps in itunes, the message said i could not sync as the software on my replacement phone was too old and i have to register it as a new phone and do a restore later. fine.
so i registered it as a new phone and itunes starting syncing my apps which took a long time. after that, i managed to update the software to OS4.3 but then my apps were all screwed up. i have 400+ apps but only 100+ came up on my phone and all my game data is lost.
gurus here, should i do a restore again? i am just worried this time, all my apps will disappear, and not just the game data...
please help... dunno what to do
iPhone 3GS iOS 4