Unfortunately, very few applications' data is stored in such a way that they are in a separate, backup-able database. That said, if I understand correctly, the data is backed up, but just does not get moved/restored during a device change.
I don't know the technical details, but no doubt anyone who has changed devices using the wizard or upgraded OS's has noticed that you lose your registration info on 3rd party devices plus all your custom settings. Yes, usually your email/sms/notepad/tasks/contacts/etc are saved but even if your 3rd party apps are successfully migrated, your reg info and settings are gone (even those that do not use registration keys, just to get that out of the way).
This is because your user settings are stored in a separate database (someone can correct me on the details), which I think is content store? User settings? Anyways, the settings are stored somewhere but by default these are not restored on an OS upgrade or device switch.
I would guess that possibly there is a way to find that database (or databases) and somehow selectively restore the data you need, but as you can tell from my untechnical explanation thus far, how to actually do that is beyond me. But I would say that it can be done.
Perhaps someone more knowledgeable can step in.
Oh, one might ask why this isn't just restored by default. Well, I have thought about that too. Over the course of time, where one is installing and uninstalling a lot of applications, all of which store their data in this way, a lot of crap can build up. e.g. you install some diary application, decide you don't like it, and delete the application. All the diary info stays, and your database of application settings gets bigger and bigger and as you switch devices and upgrade OS's, unless this database gets cleared periodically, your memory will keep going down, and the BB will get bloated. So like a Windows re-install where things get fast again (but you lose many settings and history), this database where user settings are stored gets wiped clean. Usually, that's a good thing, unless you have a large amount of data stored like you do -- and then it kinda sucks.
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