Force CKEDITOR to refresh config
For me setting CKEDITOR.timestamp = +new Date
works super fine. I wrote it in a JS that will be loaded before any other CKEditor JS will be loaded (see my custom Drupal module).
Now the query that is appended to the custom plugin or custom config JS gets refreshed every time I reload my browser. I guess that might work with custom CSS as well, but I didn't test that.
I have found a quite elegant way:
It is enough to set:
CKEDITOR.timestamp='ABCD';
just after you link ckeditor.js or anyhow before ckeditor loads all its files
this is the variable CKEDITOR uses to add timestamp to all .js .css files it loads dynamically.
So every time I change those files I update that variable and browsers will reload them.