SketchUp to Unity auto-refresh Issues (Prefabs break)

[filibis]

Hi everyone,
I have a problem with Unity's auto-refresh feature (again )
In the beginning everything works flawlessly when i save (overwrite) SketchUp (.skp) file and Unity recognises it and model gets updated without problem. However after i make some improvements in Unity (such as adding scripts to doors, creating prefabs (instances), camera movements etc) and then decide to update my model in SketchUp and overwrite the .skp file, Unity 'appears to be auto-refreshing' the .skp (i see progress bar) but nothing changes in Unity. So i end up deleting the model from the hierarchy tab and reimport manually which causes me to rearrange all the scripts and other adjustments once again.

How to encounter this problem? I highly suspect that it's because i break all prefab connections when i create my own prefab for chairs or windows (to create instances). How do i do that without breaking the imported .skp? What should my workflow be in such case?