How to remove custom module provided entity instances by the time the module being uninstalled?
A potential duplicate. 

The short answer (as I can see), you CAN'T right now remove content by the time you uninstalling the module. That makes you (us) to do it in two steps:


Write a update_hook where you remove all the content of the custom entity
You uninstall the module. 
(drush cex, which removes the module from
    core.extension.yml)