I recently reformatted the Cave Story+ IL leaderboards to allow for the many challenges (instead of just one) and adding their respective categories. However, by doing so, the leaderboads lost the current runs. I can see the runs in their "run-deleted" status at the audit log, but I can't access them to modify then and reassign it to the leaderboards. (I tried clicking the run link but both show up as N/A)

Is there any way I can recover those runs to relocate them?

Did you make subcategories or did you delete the category? In case you made new subcategories, go to the subcategory you just created underneath 'variables' and hit "Set the default for all runs without a value". Did you delete a category? The only way to get the runs back is to manually re-add the runs. This can be done by looking through the audit log and resubmitting the run.