If you have downloaded any app directly on your iPhone or iPod Touch by using the built-in App Store then you might loose those apps on syncing your device with iTunes. So here is a simple tip which will stop iTunes from deleting those apps which you directly bought and downloaded on your device by using the built-in App Store app.
All you need is to transfer your purchases from your iPhone to iTunes. You can do it in two ways!
First one is by navigating to File menu and then choose Transfer Purchases from "Your iPhone"
2nd method is more simple. Just right click on the name of your device from the sidebar menu and choose "Transfer Purchases".
Thats it. iTunes will automatically transfer all of those apps which you directly purchased from the built-in iTunes Store in your device. Now click on the Sync button and iTunes will not remove any of your purchased apps. If you still have any confusion, check out the video demo below:
You may also like to read:
How to Sync Music to iPhone Without iTunes for Free