Syncing iphone after itunes reinstall

[jamma6700]

I recently reinstalled iTunes. When trying to sync my phone I am getting the message that it is synced with another library and all content will be deleted etc. My questions are,

Does this message only apply to music? If so its fine because I have already restored my itunes library.

If this will also erase the apps how can I restore the apps back into itunes. I backed up all of the folders from the previous itunes?

Basicly I just want to get back to where I was before I reinstalled.

iPhone 3GS
Windows XP

 

[Eluded]

Regardless of music/apps, you can use the following article to download past purchases for itunes either free or paid downloads.
http://support.apple.com/kb/ht2519