Why will my apps have to be deleted to change mys ettings?

every time i try to change the settings on how i manage my music or videos on my ipad2 a message pops up saying all my apps and data will be deleted. will it really delete everything, i dont want to find out the hard way

They should not if everything works correctly.
I don't know about you but I never trust my data to everything working corectly so I always backup first before an upgrade. In fact I do it at least twice. In the case of my phortos I do it even more then that.
The installer will remove applications that are not compatable with Mavericks. You can check your applications for compatablitiy at http://roaringapps.com/apps
Allan

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