Hey @_Cri5! Sorry for the delay 
According to this post (Babylonjs Editor export without textures - Questions - Babylon.js) I just added the way to export .babylon scene files including ONLY geometries. So, using that export it can be easily loaded in server-side to compute some physics in server-side.
The only way I see (at the moment) to get custom properties in a .babylon file is to use the .metadata properties of objects (available on meshes, sounds, lights, cameras, etc.). Can you tell me kind of data you’de like to be custom data? Thanks