A feature introduced with iOS 9 referred to as app thinning or app slicing allows each device to download only the code and resources needed by that device, resulting in smaller downloads and better use of storage on the device. As a consequence the device no longer holds the universal version of the app that could be installed on any device so transferring apps is no longer supported. Hopefully Apple will make some changes to the way this works, but in the meantime you can download past purchases from iTunes and/or enable automatic downloads of app purchases to make sure that iTunes always has the apps that you want on your device. As long as you make sure all apps are present and updated in iTunes before attempting a restore there should be no loss of data. I can't confirm, but it seems a recent update means that all data is restored and apps that are not in the library are queued for download from the iTunes Store over Wi-Fi, in a similar fashion to the way restore from iCloud works.
With Macs iTunes authorization is tied to the hardware but in Windows it is the instance of the operating system. Reinstalling or upgrading Windows without deauthorizing first should be avoided.
See also Recover your iTunes library from your iPod or iOS device to make sure you don't lose any data as a result of the rebuild.
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