As far as I know (I don't know the APA style very well), you always use square brackets in English to set off your changes to the original. So in your case, it would be:
We totally refute your allegation regarding our "refusal to discuss [our] questions concerning [your] amendments to [our] VOR payment schedule at Commercial Meeting.”
Yes, it's ugly. What's even uglier is this (MLA style):
We totally refute your allegation regarding our "refusal to duscuss [our] questions concerning [your] amendments [ . . . ] at Commercial Meeting."
Yes, apparently MLA style dictates that if the ellipsis points weren't in the original, you have to set them off with square brackets. And since MLA is mostly used in liberal arts/humanities writing, which often deals with literature, there
might be an ellipsis in the original. Strange.
If it were me, I would reword the sentence so that it still refers to their allegations but doesn't quote them directly. That way, you can make it super clear. Something like this, maybe:
We totally refute your allegation that we refused to address your questions about the amendments you made at Commercial Meeting to our VOR payment schedule.
Especially since this looks like a business document. It's not like the original was copyrighted; it's just that you want them to feel like you actually listened, right?