I just checked Dragonspiral Tower on serebii...

Question

...and I realized that I was looking on Reshiram and Zekrom.

http://serebii.net/pokearth/unova/dragonspiraltower.shtml

Does it mean that you get second chance to capture them if you defeat them at N's Castle?

Answer 1

Not exactly. You must catch Reshiram/Zekrom in order to proceed in the game. If you defeat it, the game acts like nothing happened and you battle them again. (Apparently you don't get any EXP from defeating them.)

However, there is one exception: if you have a full party and have completely filled every PC box, the game let's you continue and you can catch R/Z at the Dragonspiral Tower.

Comments

what if you run out of pokeballs

Answer 2

Yeah. I'd say that, if your boxes and party are full when you catch either Dragon, then they're sent there to be caught a second time.

I know for a fact that you can't advance in the game without legitimately catching Reshiram / Zekrom, so that crosses out the idea of, "Catch them there if you don't at N's Castle".

It is very possible to have six Pokemon already, when you go to catch the legendary dragons, so this must be where they go if the box you try to transfer them to is full.

Comments

...do I have to chatch them in order to reappear or just defeat them?

Answer 3

I guess so. But right below both of the dragons it says that you can only face them if your party and boxes are full when you battle them at N's Castle.

Comments

when i caught Reshiram,i only had like,20 pokemon in my first PC box and my party was full so i had to send my mienfoo back to the PC!