Will itunes app sync really delete all apps on device?

Q: How to sync outdated itunes apps library with new apps from phone instead of the other way around?
Background: I always used app store on my iphone 3G to download. But due to its size i must download navigon through itunes. But if I download through itunes and sync apps with my iphone, i will loose all downloaded apps on the phone.
Is there a way around this? Is it possible to first sync itunes with the iphone. Then download something in itunes. Then sync the iphone with itunes? If yes, my question is: How to sync itunes with apps from phone instead of syncing the phone with apps from itunes?
Is there anyone that can help me out with this? Very appreciated

I'd first recommend going into Disk Utilities (Applications - Utilities - Disk Utility) and Repairing Disk Permissions on your internal HD. Then retry. If they still don't work then do both a SMC and PRAM reset using the following instructions:
*SMC RESET*
• Shut down the computer.
• Plug in the MagSafe power adapter to a power source, connecting it to the Mac if its not already connected.
• On the built-in keyboard, press the (left side) Shift-Control-• Option keys and the power button at the same time.
• Release all the keys and the power button at the same time.
• Press the power button to turn on the computer.
*PRAM RESET*
• Shut down the computer.
• Locate the following keys on the keyboard: Command, Option, P, and R. You will need to hold these keys down simultaneously in step 4.
• Turn on the computer.
• Press and hold the Command-Option-P-R keys. You must press this key combination before the gray screen appears.
• Hold the keys down until the computer restarts and you hear the startup sound for the second time.
• Release the keys.

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