Again, I'm not that far into my reread(relisten) but I'm pretty sure that Faile was rescued by the time Rand balefired the palace.
Doing some quick (2m) searches, yeah, Faile and Perrin are back together before Chp 21 tGS. Rand balefires the pelace in chapter 37.
I realise BS royally screwed up the timeline, but I thought it was pretty apparent that this happens after KoD.
Even if this is a bit of a retcon to fit the events, it's possible that the waves were a reaction to the Pattern burning backwards in time from such a giant amount of balefire being used to destroy Natrin's Barrow.