You have to keep hitting him, which stuns him enough so that you can get to
all the other mirrors.

The tactic I used to defeat Flaahgra was to first lock on to him, then
position myself so that the arms on the mirrors are in my line of fire.
I'd then circle strafe Flaahgra, firing as I went and strafe jumping as
necessary to avoid the plant's swipe attacks. If I came across an active
mirror, I'd zap its arm with a Missile or a Charge Beam shot, then I'd
go on to the next one, still firing as I went. Keeping up the weapons
fire would ensure that I'd stun Flaahgra at least once while I was
moving; the beast can't flip any mirrors while it's KO'd.

Just remember that you have to reacquire the lock at the beginning of
each round: just pan up to Flaahgra's face with R and the C-Stick, then
hold L to lock on and release R and C.

It's easier if you think of this fight as being like the one against the
Parasite Queen in the Pirate Frigate minus the force field and plus some
secondary targets (the mirrors and the channels leading to Flaahgra's
roots).

HTH. HAND. :)

Try here:
http://www.gamefaqs.com/console/gamecube/game/32495.html

You need to move quickly and get the other mirror off before he can
switch the first one back on.

If you think that's hard, he'll got for 3 and then finally 4 mirrors.