I ran into a seriously confusing issue with a project that I’m learning the internals of Drupal 8 for: custom contextual links were not reliably appearing or even disappearing after removing them from code, and the only thing that seemed to work was to fully uninstall and reinstall the custom module, which was far from ideal. Turns out that Drupal caches contextual link markup in sessionStorage, which is why clearing Drupal’s own cache had no effect like you would expect. The easiest way of handling this is running window.sessionStorage.clear(); in your browser’s developer console. Alternate solutions include opening the page in a new tab will cause a re-download of the contextual links (due to how sessionStorage works), or opening up your browser’s developer tools and deleting the sessionStorage entries for the entities or other identifiers - for a block it would be Drupal.contextual.block.*, while for a node it would be Drupal.contextual.node.*.