The best advice I can give you is....
As soon as you have installed iTunes and before you plug your phone in, got into the preferences and I forget exactly which tab but there is an option about auto sync phone when detected.. UNTICK this.
I have found on more than one occasion that if you phone has more than iTunes when you plug it in and it auto syncs iTunes has a habit of wiping your phone and replacing it with what is in it's library, therefore wiping any new purchases you made on your phone. The sync over wifi and auto download new purchases on iTunes relies on you having it open all the time to be told to download new purchases.
Usually, with auto sync now turned off I tend to do the following.
Plug phone in
Goto File -> Devices -> iPhone -> Transfer purchases form this device (This will put all new purchases from your phone onto iTunes)
Check what I want to have on my phone
Sync
This will ensure I put all new purchases onto iTunes before I sync up, preventing the issue of having my phone wiped in favour of the iTunes library.
Hope this helps!
When I get time I may also write a quick techdoc for people on here about moving iTunes to a new computer as it tends to be a pain and can easily loose your whole library.