Effect of Shortage of Resources on Buildings and Cities
I went into one of my late game saves and purposefully sabotaged my coal reserves to see what would happen. Even with -7 coal my cities' production was completely unaffected which would lead me to assume that a resource shortage should not negatively affect your buildings in any way, it's just going to prevent you from building anything else requiring that resource until you find another source(s) to refill your reserves.