BuildPlayer in Editor script throwing an error

I'm trying to use an automated builder script. For this script to work correctly I need it to rename some folders in the Assets directory to allow them to be compiled into the Resources folder, or to be removed from the Resources folder. This script has worked before in the past, but now on Unity 4.6.0 it's throwing this error:

 Reload Assembly called from managed code directly. This will cause a crash. You should never refresh assets in synchronous mode or enter playmode synchronously from script code.
 UnityEditor.BuildPipeline:BuildPlayer(String[], String, BuildTarget, BuildOptions)

The weird part is that it still generates a working APK file. So I'm not sure if this is really a problem, or some kind of extra enforced warning.