Hello,
When you hover over the links, does the url point to the current section's files area, or a different place? We had an issue where files stored in the main course would copy over, but they were linking back to the original. From an admin point of view nothing looked wrong, it wasn't until I went into the HTML in the RCE that I saw links were pointing to previous sections and then just updated the URL as needed. I am not sure if this is the same thing you are running into.
We use Rise for modules and each module has a presentation between 20-60 slides with activities and the like for our students to use to study and learn. However, nothing is graded in our SCORM packages, and all links are to files within our organization stored on Sharepoint or external links.
What type of activities are the Rise links trying to open?