Excluding assets of the main package from the scene asset bundle

We are trying to create scene asset bundles to be able to load some scenes over internet.
We are trying to reduce bundle size by excluding assets (Mainly textures) shared between bundles that are already included in the main package.
Asset Bundle Browser displays all its dependencies but does not allow us to remove anything thats already included in the main package. We tried creating a seperate bundle for the duplicates in order to prevent those assets from being included in the bundles, but then those textures displays as missing even if they are already in the main package. This problem occurs for textures in the resources folder as well as other folders.
Is there a way to overcome this limitation?