Hi im a painter and have come across tis problem many times,what i usualy do is brush the flaking areas.By using a roller it is causing a suction and will continue to flake.
Other than that just scrape it back and get it re skimmed.
Hope this has been of some help.
Just thought of an idea and it may be stupid but is there any reason why you cannot spray the paint on. Then the artex is undisturbed.
Spraying the garden fence was once thought to be a no-no but now it is all the rage.