Losing hyperlinks when linking word documents

We use RoboHelp version 9.0
Project description
We have a Parent project with 7 child projects. Each child project has, on an average, 40 files.
The files in each child project are linked to word documents. Every time we have updates to content, we update the word file and click Update in RH project.
All the child projects are merged in the parent project via TOC.
On completion of updates in the individual projects, we generate the individual projects and then generate the parent project for final output.
Our project structure is like this, where each circle represents a folder.
The issue
The issue we face is about See also links.
Each word file in almost all projects has “See also” topics without links in the word document. However, we hyperlink them with .htm files (within the child project and between child projects) in RH.
Because the links are set in RH and the content updates are made in linked word files, whenever we modify the word files and update them in RH, the links are lost. We need to manually go to each file in RH and re-hyperlink them. Although we select the “Preserve modifications to this file” before we save in RH, the links are still lost.
In addition to losing the hyperlinks, a duplicate file gets created for each file in backend. We have to manually delete each file.
My questions
Are we doing something incorrect in this process? Losing links and file duplication - is this because of incorrect folder structure? Is there a way we can prevent it? We tried linking See also topics in word files itself, but since the hyperlinks have an absolute path and not relative path, we lose the links if the project is placed in another computer.
The total count of files in the complete project is around 500. We tried having a single project rather than merged projects. But we are not sure if we can multi-author a single project. We use SVN as a source control tool and apparently RH does not support it.
   3.  Is linking the word files the best practice? My organization insists on maintaining word documents.

According to this, Rh is compatible with SVN.
http://www.adobe.com/devnet/robohelp/articles/robohelp_subversion.html
See www.grainge.org for RoboHelp and Authoring tips
@petergrainge

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    See www.grainge.org for RoboHelp and Authoring tips
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