The application keychain should not be deleted or altered by any means during the update. If you experience this, you must do something wrong (see Joachim Questions above).
(In fact, uninstalling the application did not remove its keychain in iOS 4.x, which usually should not happen. However, I did not check if this was improved with later versions of iOS.)
In addition, the keychain is not part of the application file system, so the update should not affect its contents. The keychain belongs to a central, secure database (in fact, it is a special sqlite3 database). For more information, see the “Key Data Protection” chapter in the Apple iOS Security document: http://www.apple.com/ipad/business/docs/iOS_Security_Oct12.pdf .
As a conclusion: your application keychain will remain unchanged after updating the application.
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