Help With Linked Objects

I created some basic assets for a medieval scene (crate, barrel, bucket - each with their own group and .blend file.) Also created are three shops/vendors, also in separate .blend files. I have linked (didn’t append, in case I need to edit them later) the basic assets into each shop file for detail. All objects in each shop are then put into a large shop group, to link into a main scene as one object, so basically the assets are linked to the shop, and then the shop is linked to a scene.

When I link each shop into the main scene, everything shows up correctly, but when I reload the .blend for the main scene, the crates, barrels and other basic assets (that are doubled linked) for the second two shop groups disappear. (See image.)

Hope this all makes sense. Is there anyway to prevent this?