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.
In order to update your publication from INDD, you have to always use the "Save online" option, once the changes in your INDD file have been made.