Now, I am a newbie (coop is arriving today), so take this with a grain of salt.
From what I've read, the idea of the DLM is to let the bedding do some composting all winter, with the chickens "turning it" when they scratch, and let the good bacteria (few bacteria are really harmful) break things down. It would probably be best not to do a very thorough cleaning, or you are just removing all the good bacteria that you got established over the winter. Some things I've read suggest only removing only part of the deep litter bedding at a time, leaving some to keep the good bacteria established.
While I am new to chickens, I am a biologist and I used to run a lab where we had many saltwater and freshwater tanks. Knowledgable fish owners never remove all of the water, but keep some of the old to keep the good bacteria at work. The animals are different, but the principles are the same. There are billions of bacteria around all the time, trying to eliminate them only throws off the natural balance. Let the good ones work for you.
That being said, vinegar is great to clean things that must be cleaned (poop covered roosts, food dishes, etc.). It is really safe and not over-kill.
