How to sync iPhone library with iPhone with deleting phone's content?

My computer's registry became corrupted so I had to reinstall Windows. I'm running the latest version. I have the latest version of iTunes too.

When I go to sync my iPhone to my computer, it won't let me automatically update new music downloads or playlist changes from my computer to my iPhone.

iTunes says,
"Are you sure you want to remove existing music, movies, TV shows, books, and tones from this iPhone and sync with this iTunes library?"
"Music, movies, TV shows, books, and tones synced to your iPhone from other iTunes libraries will be removed and items will be synced from this iTunes library."

My computer is authorized for this iPhone.

Is this just a standard warning or will I love all the save data on my iPhone for my apps? Just making sure.

The warning is standard and unless you have backups of your photos and PDFs you will loose them.

iTunes on the computer can automatically download all apps directly to the pc. Just sign into to the store, click on 'purchases' select all' then begin download. Do this for apps, music, videos, tv and books.

You can also have purchases that are currently on your phone transferred to the pc by right clicking on the device name in the iTunes side bar and select transfer purchases, this will not use an internet connection.

Anything that you had ripped to iTunes from a CD, prior to the reinstall will have ripped again.

If you have an external hard drive, I suggest that once you have followed the above steps, export the library to it. It will save you a lot of time if you ever have to do a factory reset on the pc again or upgrade to a new device.

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