In the Filings section, expand the details for the filing where you would like to replace the document. To do this, click the line item for the filing. 
Once the line highlights in blue, the details will be displayed below. Scroll down to where your document is uploaded. To remove the document, you can click the x on the far right. This will remove the document and provide you the opportunity to upload the intended document.
Click the black up arrow button to upload.
If you encounter this message after uploading the correct document, you'll just need to select Save Changes to update the section.