Yes, knowledge of events whose existence has been wiped out by Balefire remains; that dissonance is the most significant danger Balefire presents. From Moiraine's explanation to Rand in The Fires of Heaven (emphasis mine):
Fragments of manuscripts remaining from the War of Power say several
entire cities were destroyed with balefire before both sides realized
the dangers. Hundreds of thousands of threads pulled from the
pattern, gone for days already past; whatever those people had done,
now no longer had been done, and neither had what others had done
because of their actions. The memories remained, but not the
actions. The ripples were incalculable. The Pattern itself nearly
unraveled. It could have been the destruction of everything. World,
time, Creation itself.
(page 120 in the hardcover). As I read that, it was the actual mismatch between the memories held by those threads still in the Pattern, referencing threads no longer in the Pattern, that threatened the Pattern's ability to hold together.
The previous page has an example of the memory existing after the action has been excised:
You begin to see the problems, the dangers? Mat remembers seeing one
of the Darkhounds chew through the door, but there is no opening, now.