You need to be careful what you mean by 'Domain files'? Do you mean the domain.sites files that iWeb stores data in?
If you do, then the answer is no, you can't download anything from your server that will be any use to iWeb. All the files already published to your web server are html files and iWeb cannot read html files - it has no import facility.
When you publish from iWeb to a local folder on your desktop, html files are created and that is what you upload to your web host. You cannot download html files and put them back into iWeb as iWeb has n o import facility.
If you have lost your domain.sites files, then there is nothing you can do unless you kept a backup of them? If not, then you need to alter the html files of your site directly with an html editor such as TextWrangler and if you don't want to do that, then you will have to re-build your site from scratch in iWeb.
You do realise that iWeb is an unsupported product and has been for the last 4 years with no updates for the last 6?
Perhaps, if you need to re-build your site from scratch you might consider a supported application such as EverWeb. Take a look by clicking on the link.