Apps that became iOS 4-only are deleting previous app copies from phone

I've noticed that newer versions of apps that became iOS-4-only have been causing the previous iOS 3.1.x compatible version of the app to be deleted from the iPhone when syncing. I assume this is because the newer version of the app is not backwards compatible with iOS 3.1.x, so iTunes tries to replace the app on the phone with nothing, thereby deleting it.
Is there a way to prevent this? An example of this behavior is iPassword Pro 3.1.1 to 3.5 on an iPhone with OS 3.1.2.

got my apps back!! while my ipad was plugged into itunes i clicked on my device, selected the Apps tab. It listed the 5 pages of apps I should have on my ipad. I moved the last app i actually had currently on the ipad to the bottom of the last page of what I should have had on the ipad. I applied it, it went thru a Sync and they are all back on now hope it helps you!

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    Hi VeryBerry1,
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    The articles below may be able to help you with this.
    Click on the links to see more details and screenshots. 
    Downloading past purchases from the iTunes Store, App Store, and iBooks Store
    http://support.apple.com/kb/HT2519
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