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I have an iPod Touch and an iPad and use one iTunes account to manage them. Recently there is little space in my MacBook and it turns out there are too many apps that I already removed from my iDevices but still stay in iTunes. I took it for granted that I can remove all of them in iTunes and those still on my iDevices will be copied back to iTunes when I sync it next time.

Unfortunately this does not look correct. I've just synced my iPod Touch and now all apps on it are gone! I tried to restore it from a previous backup but seems the apps were not restored.

I dare not connect my iPad to iTunes again. How can I make sure the same wipe will not happen? Is there a way to tell iTunes that removing apps in it does not mean I want to remove them on my devices?

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I finally find the answer. Before syncing, select the File menu and choose "Transfer Purchases from ...". After this all apps on the iPad is copied into iTunes' app folder and you can safely sync now.

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