yes, there can be two indexes, because the addon domain has (or should have) it's own folder, both on computer level and on site level.

If f.e. the new domain is called "newdomain.com" and you have added it as addon domain through your CP, a new folder, called "newdomain" has been created inside your public_html folder. That's where you must publish. To accomplish this, in BV, in the "Folder" field of the Publish dialog box, fill in "public_html/newdomain" (without .com or .info etc)

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