Keep the wood shavings on top as mulch....if it's mixed in it will suck up nitrogen your plants need....rain/snow/watering will wash the nitrogen from poop into soil.
But Coop de Grass' question was not about outside compost, it was about "deep litter inside the coop". .......yes, it is possible that DE would decrease the macro-organisms population in a coops deep litter. Plus it makes no sense to use DE in that, and most other, situations.
Here's couple links that might help.
You might not want deep litter in your coop, deep bedding might be better choice.
TalkALittle's post on DB vs DL: https://www.backyardchickens.com/t/1075545/can-i-do-deep-litter-method-with-this-coop#post_16440037
Here's a great description of contents...