New iTunes, syncing, and iOS update questions!  Hot mess over here!

I'm in a quandary and need some help. Bare with me if I forgot details.
I moved all music to an external drive and a week later, it died.
I got a new laptop and downloaded iTunes 9.2
I've transfered all my purchased music and applications from the iPhone to my new iTunes.
_*I'm getting ready for the updates and have the following questions:*_
Some applications aren't showing up (ie. Project 365). Why would that be?
An error message pops up when I want to "sync" my applications. Since I transfered my purchases, do I ignore?
Do I need to sync my iPhone to my new iTunes before the iOS update?
If I ignore the warning messages, will the iOS update delete applications?
The iOS update has warnings. What will I lose?
I am currently running an (3 hour!)iPhone backup.
I swear I'm not that computer illiterate, but extraordinaryly cautious since losing everything.

If you did not backup prior to upgrading and the cancel button is showing, do that now. You should always backup before doing an upgrade. If it asks you to sync your apps then do that. Your backup during upgrade will take hours because itunes is sending all your data to Apple instead of just internally inside your computer.

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