Salamanders don't hibernate. In the wild, in the winter, they'll slow down when it gets cold, but they don't have a true hibernation.
Even if the burrows collapse, they'll just build new ones. It's okay. Clean the water dish daily, and continue to offer food regularly. Clean up the surface poop you find, and change the substrate every 3-6 months or so. I usually do mine in the spring (when it warms up enough to take the tank outside to clean) and in the fall (before it gets too cold to take the tank outside to clean!).