Filegroup mappings allow you to compare database that have a different filegroup structure. For more details on filegroup mapping see the topic Filegroup Mappings .
Below is the xml fragment generated for this filegroup mapping scenario:
<FileGroupSettings>
<ComparisonType>ByMappings</ComparisonType>
<Mappings>FG_SOURCE_1:FG_TARGET_1;FG_SOURCE_2:FG_TARGET_2</Mappings>
</FileGroupSettings>