BUG REPORT: collections within collections dissapear

I found this bug report on developer.blender.org:

T88678

It seems to be related, but in releases before 2.93, I only noticed this behavior once I started working and test a scene/file in Verge3D.

It provides a much better way of managing large assemblies. So if I make something like a bicycle, I would have a frame with components. So lets say the brakes, have many individual components such as cables, caliper, disc, lever etc. I want to be able to manage/link or import collections at different levels. I might also have several options within the upper collection containers. A good example of this was a watch I designed, which had multiple options for Hands, Markers/Numbers, and Bezels. So I have a Top Container that is Called “Bezel”, and then inside I have several distinctly unique bezels, but only one is present in any configuration. So I turn off (untick) the collections not in use for the given configuration. I also can tick on a different set of components using multiple “scenes” in blender.

I have been a little unsure how to best structure files for use in Verge3D. Up till recently, I painstakingly structured files with collections, and made liked proxies of each individual mesh object. It made it so all the materials can be applied in the main file to the proxy objects.

In my most recent file, I decided to use linked collections instead of linking individual proxy objects. The trade off, is that I have to apply materials in the linked files, as you cannot apply materials to collections. So I link all the files to the same material blend file, to ensure materials are not accidentally duplicated.

With blender, there is so much flexibility, that it can be difficult to grasp the best file structure workflow pipeline; especially with specific parameters needed for Verge3D output.