Since you can't comment on the documentation anymore (boo!), I'd note that if your Subversion repository allows changes to unversioned properties (e.g. edit commit messages), you can have Fisheye automatically rescan the change via a Post-revision Property Change Hook utilizing a Fisheye command-line option.
Our Fisheye and Subversion are co-hosted on a Windows server and the FISHEYE_HOME environment variable is configured, so the below works for us:
@ECHO OFF
setlocal
set REPOS=%1
set REV=%2
set PROJ=RepoName
set FE="%FISHEYE_HOME%\bin\fisheyectl.bat"
%FE% rescan %PROJ% %REV% %REV% >&2
exit
And since Atlassian Answers wasn't really designed work as a user suggestion forum, which is why I really miss the ability to allow comments on documentation, I must mark my own "question" as "answered".
Another approach to doing this would be using the /rest-service-fecru/admin/repositories/{name}/rescan-metadata REST api.
That way you can trigger the scan from any machine that can reach FishEye/Crucible via HTTP, not only from the host that's running it.
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