My iTunes has lost all my apps

Hi,
I recently had my iTunes lost all my apps and podcasts. I don't know what happened, but as far as I know I plugged in my iPhone to sync and charge, and after an hour I came back and iTunes had no apps. Of course syncing my iPhone meant all the apps went from my phone. Any idea what could cause this?
Thanks
Boz

OK, I think I didn't make my original post clear. The files are on the PC, they're in my My Music folder (complete path as you describe).
So yes, I can drag and drop the apps into iTunes, and same with podcasts (although subscriptions are missing). And then do a restore to a backup prior to the mess up. I have done this now, however it means I've lost all app data between the backup and now. Including photos, messages, Apple app data.
Anyway, I've worked around the problem, what I want to know is, how did this happen? Why did iTunes suddenly lose all my apps and podcast subscriptions?
Could it happen again?
Boz

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