Did too many experimental things on one load of dough.

I wanted to make my bread a little better. I had about one loaf worth of dough in the fridge for several days, waiting to be baked. It was a soft sandwich bread recipe, so it had honey and butter in it, in addition to the usual ingredients. I decided to take it out, effectively double it, by adding more of everything, then bake two loaves. Well, I had been using AP for a while, so I picked up some KA whole wheat flour. Therefore, since I was in the mood, I threw some in as part of the flour I was adding to the dough. I also substituted milk for part of the water, because the recipe actually called for some milk powder, and I didn't have any in it. Well, I let it ferment for a couple hours, then decided it was too late at night for baking, and put it back in the fridge, already divided in loaf pans. I figured I could just pull it out again, let it come up to room temperature and finish rising, then bake it. So, this afternoon, I pulled the pans out of the fridge and put them in my oven with the light on to warm them up and finish the final proof. In a little while, I had to leave the house, and ended up being gone for a couple hours. When I came back, the loaves had overproofed, I guess, and fallen a little. So, I dumped them out on some flour, did some stretch and folds, and put it all back in the loaf pans. Now, they are sitting out again, for the second final proof. Hopefully, they turn out edible. Any thoughts? Am I wasting my time? Is there a chance the yeasties may have run out of food and they may be too hungry to do their job?