Are you familiar with dreamweaver templates and editable regions? If the logo is in the template, then you need to modify the template file. The changes you make to the template will automatically be propogated to all of the files which use the template. If your html file uses a template, the html code will look like its commented out.
Also, you should not have to download the html fiile from your server because you should always keep a copy of all the html files on your computer.
I don't know about the SWF error.