How do you treat external cross references when moving to structured?

I'm trying to migrate some legacy documentation to structured format and want to be able to save it to and load from XML. I've had some success creating a conversion table, an EDD and R/W rules, but still have some issues.

I have a couple of files like: file1.fm, file2.fm, file3.fm and a BOOK file which includes those and a TOC. These files have some cross references (e.g. file1 may have a reference to file2). I want to be able to save each separate file to XML and preserve those references.

When I convert a file to structured with a conversion table, external cross references have the IDREF attribute empty (no value). After saving to XML, those xrefs are saved as text, without any tags.

Another question is how do I treat the BOOK file to be able to update page numbering, cross references, TOC and create a PDF version of the documentation? Or I can just load updated XML files, save as FM and treat the book as usual? What is a common practice?

Any help is appreciated!