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With iTunes 10.5 there was an issue, that you couldn't disable app syncing with your iPhone, without wiping all apps from the device.

Then with 10.6 that got fixed, and I could transfer music and podcasts and finally remove the app from iTunes.

Today I wanted to sync my iPhone again, and iTunes asked, whether or not it should transfer purchased items. I kindly declined, but the next thing it does is syncing my apps.

Is this a regression with iTunes 10.6.1?

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I gave this another shot, and on last "sync" it began deleting apps from my phone. I thought Apple fixed this behavior, but now it's happening again. –  Timm Apr 12 '12 at 9:25
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