IWeb has the nasty habit of overwritng the folder where it needs place its files. This is the reason that we suggest leaving it blank when publishing for the primary domain. The folder for the primary website is the public_htmlfolder. The folder containing the secondary will be UNDER the public_html folder. Also, it helps know what version of iWEb that you are using. This may have some bearing on the problem you are having with the site.
Iweb will overwrite the folder if given the path to do so. You will need to check and make sure that this is not happen.
If you have any further questions, please contact technical support or leave a comment at the bottom of the page.
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