It is impossible to run two help centres off the same content currently because of the limitations in linking between articles.
IF
You have two help centres A and B
AND
You create an article C linking to article D that is to be used by both help centres
THEN
There is no way to do this without duplicating the content.
When you put in a link it has to be to the full URL, there is no “internal” linking functionality.
You should be able to have the article C link to D in such a way that if you are in help centre A, you stay within it rather than it throw you to help centre B.
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It basically renders the multi help centre useless right now.