How to export gerber with milling layer in EAGLE 9?
You can edit the default job in EAGLE to add new Gerber files. 

In the CAM processor, right-click on the Gerber entry in the Output Files section of the window. This will open a dialog that will have New Gerber output as an option. 



After that, you can edit that output as you would any other - Click on Edit Layers, add your milling layer and name it accordingly.

If your Gerbers won't make sense to the manufacturer, they will ask you to clarify (as seen on point 10 of this article on JLCPCB website). At the end of the day, the only one who can say if the files are 100% valid for the manufacturing process is the manufacturer itself.