Actually the Namespace will be left alone once it has been added or changed within the *.vb and *.designer.vb file. Based on this post I went and re-verified this since I was confused as to what you were posting.If you open up a BO and add a namespace to both the .vb and the partial class (.designer.vb), the namespaces will stick, even after a partial class rebuild. I have tested this and I know that we have a lot of developers that have this as a requirement within their shops and use this logic on extremely large environments, so I am very confident that this works.
CustomersBO.vb
CustomersBO.Designer.vb
If this is how the BOs are structured, then you go in and rebuild the partials, the namespace will be left intact.