trouble syncing apps with new computer iPhone

I just bought a new computer (using Windows 7) so I installed iTunes on the computer and transferred all my music etc. from my old computer to the new iTunes on the new computer. I synced my iPhone to the new iTunes and that worked fine.
Now when I sync my phone, the Apps section is not checked and is greyed out. But when I check the box to Sync Apps, I get this message: Are you sure you want to sync apps? All existing apps and their data on your iPhone will be replaced with apps from this iTunes library. But I have updated some data on my iPhone apps since I originally synced the phone to the new iTunes. I dont want to replace the current data on my iPhone with the older data from iTunes.
Anyone know what I should/can do?
Dell PC Windows 7