Is this order retroactive?
No. The "Art of War" order only has an effect on promotions that occur while the order is active. This is not retroactive.
If I increase a soldiers Combat Intelligence will the order give me bonus ability points?
Yes. The covert operation that allows you to increase the combat intelligence of a soldier will retroactively give you all the "missed" bonus ability points from earlier promotions.
I'm not sure if you can combine the two. It's possible.
If you send a soldier on a combat intelligence increase mission while the "Art of War" order is active, then he will receive the "missed" ability points (as discussed earlier).
It is possible that this recalculation (at the time of completing the covert operation) takes "Art of War" into account, and thus also gives you missed "Art of War" bonus ability points.
If this is the case, it does seem like unintentional behavior, and either a bug or an unforeseen consequence of the retroactive calculation process.