To correct this navigate to the candidate's profile using the People Finder in onBoard. In the Record tab find the existing recommendation file and click the edit pencil. Use the "Checklist Step:" dropdown to select the other step. This will allow you to process the remaining file submission.
It is a good idea to change the names of the steps to be unique, such as Letter of Recommendation 1. You can then choose to apply this change to all existing candidates that have that checklist.