I don't know much about MyDMS but the path to the logo is probably wrong. The logo might be called from a different directory. Just double-check it.
This might work. Instead of editing the html just replace the logo with the logo you want. For example if the original logo in the html is called aqualogo.jpg, find auqalogo.jpg (grep -r "aqualogo.jpg" *)rename it to back it up and upload your logo instead. Just be sure to call it aqualogo.jpg. This way you don't have to change or upset the html.
Thxks,
dak