Icon for app is in iTunes, but the app itself is missing

iTunes says that it can not sync the apps in my iTunes library to my iPhone because it can not find the apps on my computer. So, I try to redownload the apps in the iTunes store and it says I have downloaded them already. I have the icon for the app in iTunes but my iPhone can not find them when they sync with the computer.
My mobile application folder has been erased. What should I do to get the apps and their data back? The data for the apps should still be in the back up of the iPhone (which I did a wired back up to my computer, not iCloud).

What device or mac are you using and with what OS?

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