Syncing music says will delete apps on iphone

I'm trying to sync music to my IPhone 4 and when I select songs and choose 'apply' a warning message pops up that says 'Are you sure you want to delete x number of apps from IPhone? This will delete the apps and their data? Cancel or Remove'
Has anyone else had this? Am I just not syncing things correctly? My apps are set to sync automatically, I haven't changed anything to do with Apps settings during this sync...
Thanks!

I have tried that but, as the apps does not appear in my iTunes, im not able to download them again. Then i will have to buy them (new) again and some of them  not longer excist on iTunes store.
best regards
Mikkel

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