🚀 go-pugleaf

Nicholas,

Your cross-references are internally structured as being between files
when they are initially created. When you import these individual
files by reference into your holding file, the insets still reference
the original files. There is nothing that you can do at the FM
interface level that will break that reference to the external file.
(If in doubt, create a MIF and examine the contents, especially the
inset sections).

It could be possible to create a FrameScript that would run through
your holding file, convert the insets to text and then use the
XRefSrcText property of the cross-ref to match up with the
corresponding MText marker property in the holding file and rebuild
the cross-ref to point to the new location.

You would also have to consider that any updates would have to do the
reverse, i.e. find the original inset boundaries, remove the flattened
inset contents, reinsert the updated files and then re-create the
cross-refs. 

This would not be a trivial task.

From your descriptions, it sounds like you're trying to use a DITA
construct for your documentation without actually using DITA. You
might be better off biting the bullet and going the proper DITA route.