If I understand correctly, you want the Form to continue in the process, but also have a wait for the background check. If you want to keep something similar to your current design, you could just add the "Remove Shortcuts" activity inside the success branch, which will remove that shortcut to the form (and uncheck the box that deletes shortcuts inside the Route Entry to Folder).

If you wanted to have a completely separate waiting process, you could invoke another workflow here which would do the waiting and reminding for the background check submission. This would allow you to do more processing in the main workflow and then wait for the background check workflow to set a metadata value that tells the main workflow to continue going.