Moved all my files to my portable hard drive and put them back on my computer but all downloads - music and apps - aren't showing up on my computer

I had a problem where I had to remove all of my picture, movie, and music files from my computer and now that I've put what I moved back onto my computer, I went to sync my iPod and realized that all of my previously downloaded apps and music files are not showing up in iTunes and I haven't been able to locate my apps anywhere. If I sync my iPod, will the files on my iPod transfer to iTunes or will I lose everything? I paid money for a lot of those apps and I don't want to risk losing them. Help please!!

You can transfer iTunes purchases to the computer by:
iTunes Store: Transferring purchases from your iPhone, iPad, or iPod to a computer
You can transfer non-iTunes purchased music by using a third-party program like one of thse discussed here:
Best iPod to PC

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