Editing Real Estate Photos

[Ofnuts]

Is the ambient layer the active layer?

I would suspect something like: 

• You load the "ambient" image as a first layer and then add the "flash" image above it,
  
• You make the flash layer invisible, but keep the flash layer the active layer (ie, you forget to set the "ambien" layer as the active layer). 
  
• The Color/Fuzzy selection tools would still work if you have the "Sample merged" option set.
  
• But when you try to apply a change, it goes to the active layer (still the "flash" one), and nothing happens (except a message about an invisible layer) because the layer is not visible.
  

Another possibility is that you save the selection to a  Channel. This make the channel the target of any editing until you select back a layer.

If this is not it, please post a screenshot of the Gimp UI when nothing works, showing the layers list.