Transfer app from itunes to iphone

Question

Recently installed Windows 7 as a clean install replacing Vista. Then reinstalled itunes. Then transferred my apps from my iphone to itunes.
Then purchased a large app which i downloaded to itunes. The problem is I can't transfer it to my phone.
I've re authorised the computer but that doesn't help.
When I go to the sync apps tab I get a message asking me if I'm sure I want to proceed as all of the existing apps and their data will be deleted.
What do I do?

Answer 1

This article details how to backup your itunes media:
http://support.apple.com/kb/HT1382
Once backed up, iTunes can use your backup to automatically restore your iTunes library.
This article will tell you how to recreate your library:
http://support.apple.com/kb/ht1451
Make sure you have at least one entry in whatever supported applications you use for calendars & contacts. You do not want to sync to an empty address book, as this will delete the contacts from your phone. To prevent this & generate a merge or replace prompt, make sure you have at least one entry in each calendar & contact application.
Also, before you do sync, disable auto sync when an ipod/iphone is connected under preferences(in the edit menu).
Connect your phone, Do Not Sync, at this point.
Store>Authorize this Computer.
File>Transfer Purchases.
Right click the phone in the device pane & select reset warnings.
Right click again & select backup.
Right click again & select restore from backup. Select the backup you just made. When prompted to create another backup, decline.
This MUST be followed by a sync to restore your itunes content, which you'll select from the various tabs as before.
You'll get a popup regarding your contacts & calendars asking to merge or replace, select merge.
Since you'll be restoring your itunes library from a backup, your phone should look exactly like it did before you started.