I got a new computer and whenever i went to apps on my iphone all the boxes where grayed out and the box that says sync apps isnt checked.

When i check the box it says that all apps and their data will be replaced with apps from this itunes library. This is a problem since i have a lot of games and dont wanna lose all my saves. how can i sync my apps without replacing them

There is another solution in this thread that is working for a few people and you keep your apps
Look at the post on page 2 from janofmorgan
https://discussions.apple.com/thread/2632087?start=45&tstart=0

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