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There could be a setting in iTunes which may be the cause. While the iPad is connected to your system open iTunes.
Select your iPad from the left side, then select the Apps tab in the right window.
Look to see if there is a check beside 'Sync Apps'. Put a check in the box (if not already) and perform a sync.
I kept getting the same message when attempting to sync photos. Once I put a check beside 'Sync Apps', I was able to sync without deleting the apps I installed.
Perhaps your issue is similar.
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