With the proviso that I'm not personally a player of Warmachine, I found this link to the Privateer Press forums where the truly knowledgeable people hang out:
Quite close to the top of this thread, a chap who seems to know what he's doing says:
Now the Scyir isn't a weapon master
but has flank, so in order to get the
three dice on damage (4 if you charge)
you need to have a jack be in melee
range. So the jack has to get in melee
before the Scyir activates. But if the
Jack activates before the Scyir it's
drive is useless as it will not need
to re-roll nothing.
I think that "three dice on damage (4 if you charge)" answers your question - a charging flank attack does indeed deal 4 dice damage!
As far as I can make out, multiple instances of flank don't stack, but there's no problem getting a bonus both from flanking and charging...