Problems syncing i-tunes with i-phone on new computer

I've got a new laptop as my last one died and it wasn't worth repairing.  I have set up i-tunes on the new laptop, de-authorised account on the old computer & have authorised the new laptop in i-tunes but I'm having problems syncing my i-phone.
It's not recognising that i-tunes on the new laptop is the only authorised computer and won't sync automatically. If I select manual sync, a warning message says that all existing apps and their content will be replaced with the content of the i-tunes library. Not all the apps in the library are currently on my i-phone due to the size of the apps. Help!

This is covered in the settings section of the manual:
iPhone User Guide (For iOS 5.0 Software)

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