Apps missing from iTunes. How to recover?

Suddenly, about 2/3 of my apps are missing from iTunes. Basically anything I bought in the last 16 months or so - the apps I currently actually use! I searched the iTunes folder on my laptop and the apps are not there either. Just very old ones. I tried to re-download purchases that I had already made and I get a warning that I will have to pay for the apps. I'm besides myself frustrated right now. What am I missing in the instructions to re-download something already purchased? I dont want to re-purchase all the apps again. Help!
Is there a way to pull the apps from my phone and put them back into iTunes?
Any help is appreciated.

I can confirm that right-clicking on the iPhone or iPod and choosing "Transfer Purchases" will successfully download the installed applications back to the iTunes library.
One thing to be aware - if you click on the iPhone and then "Apps", you'll see that "Sync Apps" is UNCHECKED. DO NOT CHECK IT and resync without doing a transfer purchases first or else it will also wipe the apps from your device!

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