I haven't seen any information from Apple about the app update data loss bug. I also haven't seen a solid reproducible case and/or workaround. It has all the markings of a bug that's going to be hard for anyone not named Apple to test and narrow down to a reproducible case.
Perhaps we can pool our experiences (and those of your customers) and see if a pattern emerges.
When you lost data...
1) Which device were you using: OG iPhone, iPhone 3G, or iPod Touch?
2) What version of firmware were you using at the time: 2.0.0 or 2.0.1?
3) What version of iTunes were you using?
4) Which platform did you update the app from: The iPhone/iPod Touch, iTunes Mac, or iTunes PC?
5) Did you update a single app, or did you update a batch of apps at the same time using Update All?
Perhaps we can pool our experiences (and those of your customers) and see if a pattern emerges.
When you lost data...
1) Which device were you using: OG iPhone, iPhone 3G, or iPod Touch?
2) What version of firmware were you using at the time: 2.0.0 or 2.0.1?
3) What version of iTunes were you using?
4) Which platform did you update the app from: The iPhone/iPod Touch, iTunes Mac, or iTunes PC?
5) Did you update a single app, or did you update a batch of apps at the same time using Update All?