Items in the Sequencer are Take Items, not Scenes. Take Items are copies of scenes, so your script is only changing the original scene and not the Take Item (Scene Copy).
You need to either grab the take item in the Sequencer and change it's published objects:
dim takeitem as xpTakeItem
Engine.Sequencer.GetTakeItemByID(1234, takeitem)
takeitem.GetPublishedObjectByName
Or grab the take item (or scene) on the output and change it's objects or published objects:
dim output as xpOutputFramebuffer
Engine.GetOutputFramebuffer(0, output)
Output.GetSceneOnLayer or Output.GetTakeItemOnLayer
Obviously these are not full examples, just pointing you in the right direction. Let us know if you need specific examples.
#XPression