Scene-File exceeds some internal limit and crashs the editor

In our game we need an advanced traffic system that uses node-based connections to let cars driver around.
For that we need to build and reference around 55,000 waypoints.
The build itself works fine and we store those waypoints in arrays of ScriptableObject derived classes.
All waypoints are saved in 15 different gameobjects each having a class attached and a Waypoint[ ]-Array with a length of around 1000-6000 entries.
This all works fine, but after building this information through an editor wizard and saving the scene, the engine crashs on the attempt to open the saved scene!

What is wrong here?
Is there some internal limit on how much information can be stored in the instance of a class attached to a gameObject?

i can’t answer your question but are you sure the editor wizard is generating expected results? sounds like that’s where the problems started.

Yeah, the wizard works fine, as long as we keep the cound of waypoints being processed under a certain number the scene can be saved and loaded again without any problems.

Edit:

In the Console-Editor.log the following error message is shown:
Cleaning up leaked objects in scene since no game object, component or manager is referencing them
WaypointRuntime has been leaked 1352 times.
(Filename: /Users/unity-build/Desktop/automatic-build-2/unity/Projects/…/Runtime/Misc/SaveAndLoadHelper.cpp Line: 931)

Could this be the cause for the scene not being saved properly?