@sircapsalot: this is possible, and we have automation for our application, which is built into flash. This required the addition of custom flexible handlers, which can then be called via javascript.
Linux: - chrome 54, /usr/google -chrome, pass chromedriver:
ClassLoader classLoader = getClass().getClassLoader();
File flashPath = new File(classLoader.getResource("libpepflashplayer.so").getFile());
ChromeOptions options = new ChromeOptions();
options.addArguments("--ppapi-flash-path=" + flashPath);
return new ChromeDriver(serviceBuilder.build(), options);
Windows: @user7038292 flash