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In the Podcasts screen in iTunes, there is a checkbox next to every episode (right in front of the name). In my case, they are all checked (except for episodes which have not been downloaded yet; for them, the box is greyed out).

What does this checkbox do?

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Actually, everything in the library has this checkbox, not just podcasts. – Thilo Oct 16 '10 at 5:46
up vote 1 down vote accepted

During playback, iTunes skips over unchecked songs. You can also disable syncing of unchecked songs to iPod/iPhone etc.

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I see. How do I do disable syncing? – Thilo Oct 16 '10 at 6:06
    
When your iPhone is connected, in the first tab (Summary), under the Options section, there's a checkbox to only sync ticked songs and videos. – roguesys Oct 17 '10 at 3:58

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