Steps to reproduce:
1. Download initially attached project and open it. Other attached project also reproduced the issue.
2. Select \Assets\Plugins\WP8\NativeBox2D.Windows.winmd file
3. Somehow mark it dirty to be able to hit apply button. For example tick and untick WP8Player option.
4. Hit apply button. Exception will be thrown:

System.Reflection.TargetInvocationException: Exception has been thrown by the target of an invocation. ---> Mono.Cecil.AssemblyResolutionException: Failed to resolve assembly: 'Windows, Version=255.255.255.255, Culture=neutral, PublicKeyToken=null'
at Mono.Cecil.BaseAssemblyResolver.Resolve (Mono.Cecil.AssemblyNameReference name, Mono.Cecil.ReaderParameters parameters) [0x00000] in <filename unknown>:0
at Mono.Cecil.BaseAssemblyResolver.Resolve (Mono.Cecil.AssemblyNameReference name) [0x00000] in <filename unknown>:0
at Mono.Cecil.DefaultAssemblyResolver.Resolve (Mono.Cecil.AssemblyNameReference name) [0x00000] in <filename unknown>:0
at Mono.Cecil.MetadataResolver.Resolve (Mono.Cecil.TypeReference type) [0x00000] in <filename unknown>:0
at Mono.Cecil.ModuleDefinition.Resolve (Mono.Cecil.TypeReference type) [0x00000] in <filename unknown>:0
at Mono.Cecil.TypeReference.Resolve () [0x00000] in <filename unknown>:0
at Mono.Cecil.Mixin.CheckedResolve (Mono.Cecil.TypeReference self) [0x00000] in <filename unknown>:0
at Mono.Cecil.SignatureReader.ReadCustomAttributeEnum (Mono.Cecil.TypeReference enum_type) [0x00000] in <filename unknown>:0
at Mono.Cecil.SignatureReader.ReadCustomAttributeElementValue (Mono.Cecil.TypeReference type) [0x00000] in <filename unknown>:0
at Mono.Cecil.SignatureReader.ReadCustomAttributeElement (Mono.Cecil.TypeReference type) [0x00000] in <filename unknown>:0
at Mono.Cecil.SignatureReader.ReadCustomAttributeFixedArgument (Mono.Cecil.TypeReference type) [0x00000] in <filename unknown>:0
at Mono.Cecil.SignatureReader.ReadCustomAttributeConstructorArguments (Mono.Cecil.CustomAttribute attribute, Mono.Collections.Generic.Collection`1 parameters) [0x00000] in <filename unknown>:0
at Mono.Cecil.MetadataReader.ReadCustomAttributeSignature (Mono.Cecil.CustomAttribute attribute) [0x00000] in <filename unknown>:0
at Mono.Cecil.CustomAttribute.<Resolve>b__2 (Mono.Cecil.CustomAttribute attribute, Mono.Cecil.MetadataReader reader) [0x00000] in <filename unknown>:0
at Mono.Cecil.ModuleDefinition.Read[CustomAttribute,CustomAttribute] (Mono.Cecil.CustomAttribute item, System.Func`3 read) [0x00000] in <filename unknown>:0
at Mono.Cecil.CustomAttribute.Resolve () [0x00000] in <filename unknown>:0
at Mono.Cecil.CustomAttribute.get_ConstructorArguments () [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Visitor.Visit (Mono.Cecil.CustomAttribute customAttribute, Unity.Cecil.Visitor.Context context) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Visitor.Visit (Mono.Cecil.TypeDefinition typeDefinition, Unity.Cecil.Visitor.Context context) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Visitor.Visit (Mono.Cecil.ModuleDefinition moduleDefinition, Unity.Cecil.Visitor.Context context) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Visitor.Visit (Mono.Cecil.AssemblyDefinition assemblyDefinition, Unity.Cecil.Visitor.Context context) [0x00000] in <filename unknown>:0
at (wrapper managed-to-native) System.Reflection.MonoMethod:InternalInvoke (System.Reflection.MonoMethod,object,object[],System.Exception&)
at System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00000] in <filename unknown>:0
--- End of inner exception stack trace ---
at System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) [0x00000] in <filename unknown>:0
at System.Reflection.MethodBase.Invoke (System.Object obj, System.Object[] parameters) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Visitor.Visit[AssemblyDefinition] (Mono.Cecil.AssemblyDefinition node, Unity.Cecil.Visitor.Context context) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Extensions.DoAccept[AssemblyDefinition] (Mono.Cecil.AssemblyDefinition definition, Unity.Cecil.Visitor.Visitor visitor) [0x00000] in <filename unknown>:0
at Unity.Cecil.Visitor.Extensions.Accept (Mono.Cecil.AssemblyDefinition assemblyDefinition, Unity.Cecil.Visitor.Visitor visitor) [0x00000] in <filename unknown>:0
at AssemblyUpdater.Steps.AssemblyUpdaterStepBase.Apply (AssemblyUpdater.Core.AssemblyUpdaterContext context) [0x00000] in <filename unknown>:0
at AssemblyUpdater.Core.AssemblyUpdaterPipeline.Run (AssemblyUpdater.Core.AssemblyUpdaterContext context) [0x00000] in <filename unknown>:0
at AssemblyUpdater.Application.Program.CheckForObsoleteAPIUsage (AssemblyUpdater.Application.CommandLineSpec config) [0x00000] in <filename unknown>:0
at AssemblyUpdater.Application.Program.Main (System.String[] args) [0x00000] in <filename unknown>:0
UnityEditor.DockArea:OnGUI()