Relinks structure-based cross-references to marker-based cross-references.
The FM2DITA tools are designed to process unstructured content to DITA. If you are starting with structured FM files, you will likely need to strip the structure from the files and continue by using the object to element based mapping provided by a conversion table.
However, before stripping the structure, you should run this command to transfer the cross-ref linking from the structured model to markers.