How to stop iTunes 9 from deleting all my app data ?!

I used to sync my phone to two computers:
- Media and apps on my iMac
- "Info" (Calendars, Contacts) and Photos on my MacBook Air.
I simply had different items checkmarked for synching on the two machines.
This worked perfectly until iTunes 9. With 9, when I plugged into my Air to synch my calendar, it started copying all my apps to the laptop! I simply canceled that.
NOW, when I connect back to my iMac, the phone instantly and automatically starts deleting all my apps and replacing them with fresh copies! I am losing ALL my vital app data! (Plus it started installing tons of unwanted apps that I had unchecked--which will fill up the phone at some point.)
How can I stop this automatic deletion? I've now downloaded the 9.0.1 patch but I'm afraid to even plug in my phone again!
Before canceling the synch, I've already lost everything through the "A's" including some vital work stuff and hours of hard-earned game progress. Some could be recovered via TIme Machine and restoring an older backup... but I have some really important stuff on my phone since that last backup, and I don't want to wipe it.
Thanks for any advice.

Wiping my phone, restoring from backup, AND wiping all iTunes related files (from a search in Library and in Music) seems to have stopped this behavior.
(I couldn't wipe the iTunes files on the machine with my media and apps, but I did so on the other machine--where I only sync contacts, calendars and bookmarks. My iTunes library is empty there anyway.)
I don't know if this relates to an "app synching" issue that iTunes 9.0.1 fixed. Could be.

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