This can happen from a number of different possibilities. 1. The Stage 2 application was not generated from the stage 1. Either a link of the application was copied and used to submit the application or there was more than one stage 1 application and the one that generate the stage 2 was deleted accidentally. 2. If the Stage 2 was initially declined upon consideration then it separates from the stage 1. If it is rolled back to pending it will create a new request.
When this happens you will need to copy the information from the request created by the stage 2 and update the information on the original request.
Any documents can be downloaded and then uploaded to the correct request.
Once you are sure all the information has been transferred you can delete the new request that was created.