So at least in my case the behaviour where scripts go missing is somewhat by design. The BuildPlayerOptions has a property where you can set a path to the assetBundleManifestPath, a file which is built when you build out asset bundles which describes all of the scripts referenced within the asset bundles: To fix the issue, there is a different way to call the BuildPlayer.BuildPipeline method which I wasn't aware of where you can send in a BuildPlayerOptions struct, and note that this is different to BuildOptions. Nothing was referencing the scripts when the player or app is built because the script references are somewhat hidden within asset bundles, the build pipeline is not aware of them and they were being stripped. So my bug report was escalated to a senior dev and they've gotten back to me with some info about why in my case the scripts were being stripped. create a project that has two scenes, a scene called LaunchScene which has one job, to load a second scene BundledScene, which is a scene that we'll store in an asset bundle, code example to load the second scene: It's as though under these circumstances that the script address (class, namespace and assembly name) is not being stored in asset bundles. the app is built manually using the BuildPipeline.BuildPlayer method which we must use for our very extensive compiler pipeline IL2CPP is the active scripting backend, which we must use for platforms like Switch

What I've found is that if scripts are located in a package with an assembly definition, any scene that is bundled inside of an asset bundle can not find a reference to any scripts in that package, if: The referenced script on this Behaviour (Game Object 'SomeObject') is missing!

We get a heap of logs that scripts are missing when our scripts are added to assembly defintions and referenced in a scene which lives inside of an asset bundle:

I'm in the process of submitting a reproduction project. I have however narrowed down the source of the issue which you all might find interesting because it could explain why some of you are having issues. any of the suggestions listed here were not helping my case. I found this thread due to a similar issue where any scenes I have which live in asset bundles were unable to find references to scripts which live in an assembly definition.

R unity asset bundle extractor.