what unity does is read all your assets from the assets folder, recompile them and rework them for the current selected platform. since, for a project to survive only the Assets and ProjectSettings folders are relevant, everything else gets regenerated on deletion and put into the other folders in your project (temp etc.).
The only cullpit could be changes in the ProjectSettings Unity might have done which only ruins THEM then (happened to me during some beta versions on Unity 5.3 I think), but will not destroy your stuff.