What do I really lose if I backup my iPhone to iTunes without transferring purchases?
I understand the apprehension!

In reality, though, you do not stand to lose anything. The only reason to transfer those purchases to your computer would be to save bandwidth and time by not re-downloading everything. You will still lose associated app data (e.g. login information, cache, etc.), but that would happen even if you did back up those apps to your computer.

In short, you will be fine without transferring purchases.

Hope this helps!