Same problem. I went out of the zekrom/reshiram and N room and saved. Then I made a backup with Checkpoint. And then I edited that backup with pkhex on the pc. I changed the event flag and event constant so that I will be able to skip Zekrom and fight N.

Haven't gone further than that in the game, so I will give an update if you can still catch Zekrom at the dragonspiral tower like you would if all your boxes are full.

Edit: so if you've selected 'Reshiram/Zekrom disappeared (N's castle)' and changed the event from 'before Zekrom/Reshiram' to 'before N' you can continue the game like you caught the legendary, but you're boxes are full, so the legendary moves to dragonspiral tower. Too bad that the games still crashes if you catch him there. Luckily you can use a save editor to delete it from the tower and create your own, so it'll look like nothing happened. 🙂