First, export your existing content campaign. Make sure your include "Story Reference" in exported data.
Then you load that module in your content campaign, load the story entry you want to create links in and link them to the Story Reference entry. To list the Story reference entries you need to view them from the Library->Module Name->Story Reference.
Once you've linked to those you export again and the new module will contain valid links. The reason is those Story reference entries will maintain the same IDs for the most part unless you start deleting/adding newones/etc.
Story Reference entries do not show up in the Story list. It's hidden, specifically for this purpose. I use the same method on the 2E PHB.