That dark liquid is simply a natural byproduct of the fermentation process. When I first started experimenting with homemade bread and starters a few years ago, I panicked when I saw this exact dark layer and thought my batch was completely ruined. However, it is just a sign of active yeast activity. To fix this issue and continue with your meal prep, you simply need to stir in a pinch of white sugar to reactivate the culture before baking your loaf.