Based on your own answer instead of copying the original ThemesResources.xaml I'd create a new one and merge it with the original.
Create a new Resource Dictionary (e.g. FixedDictionaryResources.xaml). In Visual Studio you need to create a Windows Phone Page or use any other template that creates a XAML file. In Blend you can create a resource dictionary directly. In VS you need to remove then all the content and put in the following code. In Blend just add the
<ResourceDictionary
xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml">
<!-- Resource dictionary entries should be defined here. -->
<SolidColorBrush x:Key="PhoneBackgroundBrush" Color="{StaticResource PhoneBackgroundColor}"/>
</ResourceDictionary>
Open App.xaml and add the following code to merge the new dictionary with the default resources dictionary.
<Application.Resources>
<ResourceDictionary>
<ResourceDictionary.MergedDictionaries>
<ResourceDictionary Source="Resources/FixingResourceDictionary.xaml"/>
</ResourceDictionary.MergedDictionaries>
</ResourceDictionary>
</Application.Resources>
Reopen the pages that are still showing the PhoneBackgroundBrush missing issue and everything should work now.