You can update your publication anytime, by following the next steps.
Make the modifications on your original PDF. All the pages of the PDF must have the same dimensions - height and width.
After the changes have been applied on your PDF, you have to go on the platform => Edit => My publication => Update source and upload the modified PDF.
Make the changes in your INDD file, then click “Save” in the Webpublication InDesign Plugin. Do not click “Save as”, because this will generate a new publication and your INDD file will be linked to this new publication.