Unintentional Website Duplication = Google's Penalty

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Over two months ago I moved MysiteDotCom to a new host.  This host uses
cPanel control panel on their shared Linux plan.  As part of the setup
routine, I was provided with an alternate URL (due to the way cPanel is
setup) allowing me to directly access my website based on the server URL:

Something went wrong with the initial account setup and the following

(1) If one enters my server based URL ServerDotHostnameDotcom/~username, it
comes up with Google's PR6, which is the PR for MysiteDotCom.

(2) If one checks Google's cached snapshot of
ServerDotHostnameDotcom/~username, the snapshot of MysiteDotCom would be
displayed and the note would read: "This is Google's cache of MysiteDotCom
as retrieved on [date/time].

(3) Backlinks for ServerDotHostnameDotcom/~username would show the backlinks
for MysiteDotCom

(4) The info command for ServerDotHostnameDotcom/~username would show the
results for. MysiteDotCom.

Two months ago, soon after MysiteDotCom was moved to that host, Google
imposed a penalty on MysiteDotCom - it disappeared from SERPs for major
keyword terms.  The problem I described above could be the reason for that
as an unintentional website duplication was created.

What course should I take?


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