@He7d3r reports at https://phabricator.wikimedia.org/T59512#1212072 that there was a lag time (3 days) before Special:WhatLinksHere on a file page reflected that Flow did (in two ways actually, one a file include and one a simple link to the file).
In the code, this is apparently immediately on save (this is 'reference.recorder'), so I'm not sure what would cause this lag.
