Unprocessed Assembly-Csharp.dll not found -- Windows Store

I released a game on the Windows Store. It seems to work fine for the most part, but I wanted to make a few changes. I noticed that any changes to the code I made didn't get applied. Changes to Unity GameObjects did get applied, however. For instance, replacing one graphic with another looks correct, but changing any actual code changes weren't appearing. Everything is working in Unity's Play Mode.

I did a clean build to try and determine the problem. The clean build cannot find Assembly-Csharp.dll in the Unprocessed folder. This makes me think that the Assembly-Csharp isn't updating when I do the build in Unity.

I'm not really sure what else to try. There are very few issues like this I can find online. I am happy to provide more information, but I'm not sure what is important in this situation.

Unity version 5.0.3p3 Building Windows Store 8.1