Interesting, looks like WordPress returns urls depending on how the currently active site is configured. This might be a core bug, as the get_permalink($id) call is used by ajax search pro to always get the correct links.
I believe the best solution is to create filter to change the permalink in the results if the [Help site path] is detected in the URL pattern. I would recommend trying this code:
Change the $url variable value to the help site url. If it's detected in the final url, this snippet will try to change it to the regular non-permalink URL.
I haven't had a chance to test this code, so please be careful when editing the files.
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