When I use a custom URL in the board settings to use a self generated help page, the nav tab on help pages index is doubled. The default link is remaining but both old and new links lead to the new custom page.
This is fairly expected with what you've done -- you've added a help page for what is already a help page. If you want to use a custom URL, it's expected to be separate and thus not listed in the help system. You should probably just customize the standard terms page.
Understood.... although the logic behind that is not very clear to me. If I use a custom page and fill in a new URL I expected the default link to vanish. But thank you for the fast reply, I was able to get this resolved quickly.