There is no bug here. When you switch integration you must do several things most of which require backend work on the database. Your not suppose to be able nor is the product designed to just switch integrations on the fly.
As far as the upgrade script its just that an upgrade script meaning it upgrades your current install it is not support to move files to some new directory. There is nothing about that upgrade that suggests we are moving files to some new data directory. In fact your the first person whom has made this assumption which it was a bit confusing to me where you thought this was suppose to happen. Yes as always you can move a directory yourself.