You are correct Wendy – IDX embeds the cross-refs into each file where appropriate. The notes Jan Wright and I prepared did contain more information on this in an earlier draft and in case it helps, I’ve copied that below. We removed some of the instruction from our paper in the interest of brevity. For anyone who hasn’t seen our paper on embedding into multi-file Word you can access it via my website: https://www.roundhouseindexing.com/resources.html

Cross references: Index Manager does not combine multiple see/see also references into one cross-reference with multiple targets. Combine complex see/see also references and create generic cross-references as a very last edit to the Word files when you know you will not be taking the files back into Index Manager.
The combined index can contain multiple see/see also cross-references where the target is in more than one chapter or points to other topics. For example:
{ XE “Dogs“ \t „See also Wolves” } (Cross-references can have only 1 target in Index Manager)
{ XE “Dogs“ \t „See also Coyotes” }
But you want this result in the final index:
{ XE “Dogs“ \t „See also Coyotes; Wolves” }
To get this final result, you have to edit the see also entry in Word to combine Coyotes and Wolves. Edit one of the cross-references the way you want it, and delete the other one.
Here’s an example of generic references which Index Manager does not allow:
{ XE “Dogs“ \t „See also specific breeds of dogs” }
This type of generic reference is not allowed in Index Manager and must be added in Word. (Or you can enter them as a regular index entry in the main head, and later change the entry once you are finalizing the index in Word and not going back to Index Manager.)
Once you have finalized your work in Index Manager, you can edit the entry for the see/see also in Word once you have exported. Edit the entry itself in the Word files by searching for the pieces of the entry, and editing it in the XE field. If you re-open these changed Word files in Index Manager after combining a see/see also reference or adding a generic see/see also reference in Word, Index Manager will turn those unacceptable cross-references red in the Xref window. It will also delete them from the next export so you could lose the references if you are re-exporting from Index Manager. The best practice is to combine complex see/see also references and create generic cross-references as a very last edit to the Word files when you know you will not be taking the files back into Index Manager.