The problem appears to be that the abilities only updated AFTER each player move.
I have noticed that if the player has 1 Rail Gun and 7 Rogues, and the enemy attacks first and converts the Rogues to Rail Guns, hovering over ALL of the converted Rogue attack queue status at the bottom shows that ALL the converted Rogues are missing the ignore defense and power shot abilities. However, AFTER the player makes the first move, then ALL the Rogue have there abilities updated correctly.
If the player has another unit type that is faster than the Rogue, so moves before the Rogue, then this does not seem to be an issue, as the move of the other unit then gets the abilities on the converted Rogues updated correctly.
Judging by the general behavior when auto-resolve is used, it's as if the abilities are updated on the server okay, but are not transmitted to the client until AFTER the player makes a move. I.e. the human player is not able to use the ability as the game within the browser has not yet been told the player can make that move.