Before you attempt what I'm about to suggest, make a backup of your project.
I've never been in your situation, but if I were, this is what I would try before investing a lot of time in one-at-a-time restoration of the links.
Exit RoboHelp.
Make a backup of your project folders.
Open your project folder in Windows Explorer.
Locate the "RHWordDocs.apg" file.
Open the file with Notepad.
Theory: if you find the <word_doc> section for each of your linked Word files and change the value within the <file_name> tags, RoboHelp will restore the links to your Word documents.
-----------------------
<snip>
<word_doc>
<file_name>S:\Disaster Recovery Planning\EPIC\Enterprise Electronic Medical Record_EPIC.docx</file_name>
<snip a bunch of stuff>
</word_doc>
</snip>
-----------------------
Save the "RHWordDocs.apg" file and then exit the file.
Open your RoboHelp project to see what happens.
I've never seen the data that is stored within the .cpd file so it's possible the old paths are stored there. I don't know if opening the project with the updated "RHWordDocs.apg" file will rewrite to the .cpd file or not so, if the You may also have to delete your .cpd file.
Good luck! Please reply to this thread if this works (or if it doesn't too!)
Paul