Recently wiped HD and reinstalled everything; cannot find my apps in iTunes

Question

After a terribly unpleasant mishap with my old OS; I was forced to wipe my harddrive and start from scratch. So, I repartitioned my drive, set up a dual-boot system with Ubuntu Linux and XP (XP pretty much purely to use iTunes to manage my iPhone 3G).
Since reinstalling iTunes, however, I no longer have a list of the Applications I own - not ones previously purchased on the app store, nor ones I've purchased since then. I had to authorize my computer again, and now iTunes reports two PC's being authorized. However, there is only the one. I'm not sure, but I suspect this could be related.
It seems iTunes feels this is a new, second computer. This is very inconvenient, however, because since the HD was wiped and everything reinstalled, I cannot go back and deauthorize.
Also, as I have no apps in iTunes (though my account on the app store does show my app purchases) I fear if I need to remove an app from my iphone for whatever reason, I'll have to purchase them again rather than just re-sync them.
Under Devices>iPhone>Applications, there are non listed in iTunes. Clicking "Sync Applications" warns that it will wipe the apps off my iPhone - clearly, not the way to go.
How can I fix this? How can I get my apps back into iTunes, and how can I deauthorize the original "computer" (which no longer exists)? Seems silly to permenantly lose an "authorization slot" (for lack of a better term) just because I repartitioned my hard drive.
Thanks!!

Answer 1

Thanks for the quick reply! Knowing I can simply un-authorize everything if needed (even if only once a year) is good; I just wanted to be sure those potential authorizations were not permanently lost.
In regards to the apps, I followed the advice in the article you linked, however, my results differ: My iTunes does not say I've already purchased the app, and says I will be charged. While I could download them all, get charged, and report each in turn, that seems to be a rather poor way to go about things... and will result in my wife and Keeper of The Credit Card Finances stabbing me with sharp pointy things.
Still, opening my Purchase History page in Account Information clearly lists each purchase.
The article you linked includes this:
[quote]If you normally sync applications to your device from one computer and then connect it to iTunes on another computer, iTunes will not attempt to sync applications from that library. Applications can only be synced from one iTunes library. If you are connected your iPhone or iPod touch to an iTunes library that you don't normally sync with, you can still transfer purchased applications from the device by choosing File > Transfer Purchases in iTunes.[/quote]
Could it be that my account feels that my applications are being synced to my old installation (the one that no longer exists)? This would explain why my iTunes now doesn't even have an Applications tab under Library. If so, how could I resolve that?
Thanks again!