It is possible that iTunes is slightly confused by what is and is not already on the device. In such cases it may think there isn't enough room when there should be. These steps will usually resolve such an issue:
- Backup device.
- Restore as a new device.
- Restore the backup made earlier.
You should copy off the contents of the camera roll first unless you have Photo Stream set up and it reliably captures everything. It also assumes that all media content on the device is in your library. If that might not be the case see Recover your iTunes library from your iPod or iOS device.
Apple's official advice on duplicates is here: Find and remove duplicate items in your iTunes library. It is a manual process and the article fails to explain some of the potential pitfalls such as lost ratings and playlist membership, or that sometimes the same file can be represented by multiple entries in the library and that deleting one and recycling the file will break the other.
Use Shift > View > Show Exact Duplicate Items to display duplicates as this is normally a more useful selection. You need to manually select all but one of each group to remove. Sorting the list by Date Added may make it easier to select the appropriate tracks, however this works best when performed immediately after the dupes have been created. If you have multiple entries in iTunes connected to the same file on the hard drive then don't send to the recycle bin.
Use my DeDuper script if you're not sure, don't want to do it by hand, or want to preserve ratings, play counts and playlist membership. See this thread for background, this post for detailed instructions, and please take note of the warning to backup your library before deduping.
(If you don't see the menu bar press ALT to show it temporarily or CTRL+B to keep it displayed.)
The most recent version of the script can tidy dead links as long as there is at least one live duplicate to merge stats and playlist membership to and should cope sensibly when the same file has been added via multiple paths.
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