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.
It basically renders the multi help centre useless right now.