Apps deleted

Hi folks,

I have a big problem: few months ago I've bought from iTunes (on my mac book pro, not directly from iPhone) using an iTunesCode, the Tom Tom Europe App for iPhone.

After I've updated the iOS (Mountain Lion and the last update) and iTunes I dind't find it anymore on iTunes, but it is still on my iPhone.

How is possbile? If I will change my iPhone with another one, will I lose all the apps (inc. the TomTom one)?

The biggest problem is that now I have to make the updates and because my iPhone is almost full, I cannot donwload it directly from it, so could be good for me do it from iTunes.
Can anyone help me?

Regards,

Dan