Yes, you can manually trigger the Auto Link creation scan for existing Auto Link Rules. There’s no need to delete the Auto Link Rule and then re-add it to trigger the scan.
To manually trigger the link creation scan, click on the small setting gear next to the “Keyword” for the Auto Link Rule that you want to trigger the scan for. With the settings open, click on the “Save” button. Since the settings haven’t changed, Link Whisper will just do a scan to make sure the Auto Links are created on all possible posts.