When reopening a scene the models can appear as cubes if the game settings do not include paths to the source MDL files.
This document explains why models can appear as cubes instead of props when importing VMF or MDL nodes.
Bringing life to your scenes
Detailer is a detail sprite primitive plugin with exporters. The tools allow you to either create VBSP files, and will also create geometry that exports into the Source Game Engine with the Wall Worm VMF exporter.