I don't think we can be of much more help; I don't believe there are any low-carb, low-fat chocolate chip cookie recipes here. Please consider following one of the proper low-carb plans that are supported here such as Atkins, Protein Power, Dr Bernstein's, etc. They are ALL appropriate for diabetics.
I would never try making cookies without plenty of fat; either butter or coconut oil. I would also never add flax seed to cookies. Flax has a nutty taste that lends itself well to buns or muffins for a "whole grain" type of taste, but not to treats like cookies.
Do as Rosebud suggested and look at the recipes for almond flour cookies, then add some chopped 90% Lindor chocolate for chocolate chunks. I would take bitter chocolate like that over sugar alcohols seven days a week and twice on Sunday.
Chances are those sugar-free chocolate chips have maltitol, which is murder on my guts because they're partially absorbed - which means, as others have mentioned, you can not just subtract them from your carb count. Seriously - the small amount of real sugar in a Lindor bar or just plain Splenda is better.
You say you don't like almond flour, but it's mild flavoured and makes for the best baked goods. An alternative would be a coconut flour cookie recipe, but you absolutely MUST add lots of butter or other fat, because it is really dry.