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Apr 12, 2015 3:02 PM in response to comealongpieby Jason L,Hey there comealongpie,
Welcome to Apple Support Communities.
From what I gather, your’e trying to free up some storage space on your iPhone using iTunes on your PC, and you're concerned because apps aren't being deleted from iTunes on your PC. Take a look at the article linked below which clarifies the process of syncing and organizing apps on your iOS device using iTunes.
iTunes 12 for Mac: Sync and organize iOS apps
Also, take a look at this article which will walk you through the process of deleting apps from the device itself.
Delete music, movies, podcasts, and other content from your iPhone, iPad, iPod touch - Apple Support
Cheers,
-Jason
