From what I'm reading on the wiki it seems that level 1 makes all weapons on both sides neutral affinity to each other, level 2 makes the enemy's advantage turn to neutral, and level 3 makes them turn to disadvantage if they have advantage.
Also based on the wiki's wording of things(which I don't know if it's the same as the ingame, never noted if it was the same for other skills), this effect even applies to things like gem weapons(since weapons are treated as skills in this game as well IIRC), Triangle Adept, etc. (so people with advantage and Triangle Adept would get the increased penalty but not the bonus because Cancel Affinity overrides that)
It DOES have an unfortunate side effect of making you unable to have natural advantage anymore though if I'm understanding it correctly, but it removes your weakness to WTA problems.