Failed to parse UnityEngine.Matrix4x4 (Windows 10 UWP)

I’m working on a game in Unity 5.3.5f1 that needs to be built for Windows 10 Universal (UWP). I like to build the project to the same folder each time so that I don’t have to re-associate the app with the store, mess around with icons, etc. However, when I build my project to the folder that I’ve used for previous builds, when I build the Visual Studio project, I get this error:

Internal compiler error: Failed to parse 'UnityEngine.Matrix4x4,UnityEngine, Version=, Culture=neutral, PublicKeyToken=null'

I have tried clean, rebuild, and restarting VS but this doesn’t resolve the issue. The way I have been working around this is by deleting the contents of the build folder and building from Unity again. This is very inconvenient - any suggestions?

This issue seems to be fixed in the latest 5.3.5 p2 patch.