The thing about the first Xindi weapon was that perhaps it was a failed attack... they thought the power yield was enough to destroy the planet but it didn't, or that the generator was damaged due to some technobabble and wasn't working at 100%. Considering that the Xindi weapon survived in Twilight but the first weapon self destructed may indicate that the attacker knew it failed and activated a failsafe to prevent it from being captured.
Of course, I may also have forgotten the script and the council did mention it just being a test.
Of course, I may also have forgotten the script and the council did mention it just being a test.