For various reasons, I've only just updated to iOS4.
There are a number of games that I have gained achievements for, it is possible to update the game center app to recognise these achievements automatically?
I am not aware of a way to force the updating other than running the apps to see if they will update things as a matter of course. Some app developers store the achievements in a way that they flow back from the game center - but it's more about how each developer chooses to use all the Game Center options.
Look for a much better experience when iCloud allows developers to store more app data in the cloud so you don't have to export/import and otherwise work to get your settings and loot to a new instance of the same app.
An alternate tack is to dive into the library of each app using a tool like PhoneView. You don't need to jailbreak the device - but often can find the folder where achievements are stored and you can put them back when they go missing.