What LaTeX packages are available for ISO quality system documentation?

You may be interested in Peter Wilson's iso package. From the readme:

The iso class is for typesetting ISO International Standard documents according to the requirements specified in "ISO/IEC Directives, Part 2, Rules for the structure and drafting of International Standards. (Fourth edition, 2001)".

If the cross-reference integrity checking is the only problem, may be the package xr in CTAN would be of help.