I first noticed this issue when using Drush to enable a module. Drupal core will present a warning displaying something along the lines of:
orphaned actions (comment_publish) exist in the actions table. Remove orphaned actions
The answer wasn't readily Googled, but after some quick digging I found 2 solutions.
Method 1
Login as user 1 aka 'admin' and visit: http://yourwebsite.com/admin/settings/actions/orphan.
Method 2
This method can be done anywhere you can execute PHP. This same code is run when you access the page in method 1. I have provided the code in a format which you can paste to Drush, but feel free to pull out the function and use it manually.
drush php-eval "actions_synchronize(actions_list(), TRUE);"