Looking for some OSX iTunes sync help

[LEFT]My computers:[/LEFT]
[LEFT]- A Mac Pro tower running OS 10.6.8 and iTunes 10.5.2 (11).[/LEFT]
[LEFT]- A vanilla MacBook also running OS 10.6.8. and iTunes 10.5.2 (11).[/LEFT]
[LEFT]My device:[/LEFT]
[LEFT]- An iPhone 3GS running iOS 5.[/LEFT]
[LEFT]I always synced the phone to my Mac Pro. Today I plugged it into my MacBook to charge it. Sometimes when I do this, iTunes opens automatically, and I close it to avoid syncing. Today I got a message I never saw before, one I assume is part of the newest iTunes: it said (and sorry I can’t get the exact message) something to the effect of needing to authorize this computer.[/LEFT]
[LEFT]I Google this and learn that apparently, I can authorize up to 5 devices, and stuff will sync when I plug my phone to any of those devices. So I go ahead with this and let the sync happen.[/LEFT]
[LEFT]After the sync, I lost a lot of music and apps. Not everything, but there’s no rhyme and reason to what I did lose. As an example: I lost the Bastion soundtrack, which I purchased from Supergiant and transferred to iTunes. I also lost the Podcaster app which I got from the App Store. And the Blizzard Authenticator. But again, not everything; some apps and music remained.[/LEFT]
[LEFT]However, now I’m nervous. My Mac Pro should still have all the apps and songs I lost, but what happens when I plug my phone back into it? Will I suddenly lose everything there too?[/LEFT]
[LEFT]Any help would be super-appreciated, as this issue has left this Apple supporter rather jaded and nervous.[/LEFT]

From what I can tell, it seems as if it reset everything. Thinking that you wanted to sync your phone to a new iTunes library, overwriting your old one.

That said, what did Dr. B say?

What’s weird is that the wiping was arbitrary. You’d think in such a case, the second computer would use what is in its library as a basis for sync. It partly did that, but some recent apps I got, like the official Gmail app, weren’t deleted.

Dr. B wants me to figure this out on my own. He believes it will make me stronger. But not strong enough to defeat Dr. B. Let’s not be silly, now.

No idea why it’s like that, though I beleive that some apps are more easily transferable than others (usually the free ones).

Well excuse me, princess.

Someone on the Apple Support Boards helped me out. Basically, all I had to do was re-sync with my Mac Pro tower and it gave me back everything. Lesson learned!

For anyone who may also need the answer:

Thread’s existence now simultaneously realized… and defeated.