Syncing To New Computer - App Data

I am trying to transfer my iPhone 4S with a new computer as my old has Mac died.

I managed to copy my music to the new computer using Senuti, and have transferred all my apps over using the "Transfer Purchasses" option. All my other data, like Contacts, Calanders, etc are all in the cloud.

So today I thought I would have a crack at trying to sync it to my new MacBook Pro. I plugged it in and managed to sync all my music, photos, and movies without any trouble and I can now put new music on my iPhone.

I am a little worried about the Apps though. As I said earlier I transfered all the Apps to the new MacBook and they are currently sitting in iTunes.

When I plug in my iPhone they all appear in the App section and I can re-arrange, add and remove stuff without any trouble and they sync to the iPhone without trouble.

What I am worried about is that I am getting an replacement iPhone sent to me in a few days and was wondering if the app data is being backed up when I do a back up.

The reason I am worried is that when I go to the "iTunes Wi-Fi Sync" on the iPhone, it states that my Apps are still synced with my old Mac, while my Books, Movies, Music, Photos, and Tones are synced with my new MacBook.

I never use "Wi-Fi Sync" but it does state that I last backed upp my Books, Movies, Music, Photos, and Tones today, while my Apps where last synced on my old Mac two months ago.

So what I am really asking is my App Data being backed up, so I when I get my new iPhone I will still have my App Data?