Yes during DXF Import you need to "check" the layer option "Flash" for the Drill layer. ACE outputs a drill hit for each "Gerber Flash" that is contained on the layer that you have checked "Drill" (on the export layers option). https://support.numericalinnovations.com/support/discussions/topics/14000002565
Here's a video using ACE how to quickly convert those drawn Gerber circles to flashes, and then output the drill file.
Note: Truthfully it would take a manufacturer 30 seconds to convert those circles to flashes and output drill data. Many manufactures will perform this task for you automatically in their CAM (as it takes less time than contacting the customer to report the problem).