I actually tried this a while ago. If you deleted the apps, they do not come back. If you kept them installed, they stay there.My DSi XL came with Flipnote Studio and Photo Clock, to name some... no app appears on the DSi Shop to re-download. I guess formatting system could bring it back? Else that system has lost Flipnote until hacked.
Once I formatted its system and all the built-in apps were kept, but dunno if you uninstall them.








