I believe I need a little more info on Vil's playing type, and your image at the table at this point. This bet is a little on the larger side, but is still within mean to call with most of your range. With that said, I'll go with what I would do majority of the time when considering playing style factors....
I would make the call just as you did, now with this specific flop, and being HU. I wouldn't eliminate a donk bet here. You have low pair, on a wet, unconnected board (Based off Vils possible range). If you donk bet you are advertising a T. You have the nut flush draw at this point, and since it was a 3Bet pot, I really don't think you need to bet big... even though I've taken 1/2 bets completely out of my game, you could go half pot here figuring you're donking into an aggressor. If you don't take this line often, you are advertising top pair at least. This is why I need to know more about Vil playing style, and your image. If he's a bully LAG, and you donk into him with these holding. he's going to take that as a threat to his bully style image, and inflate the pot IP. The last thing we want is be playing a 3bet pot, on a 2Bet Flop, OOP. Now, if hes a typical TAG or NIT, chances are he just calls or folds. We protect our range, advertising the T, thus Vil could possibly eliminate the flush draw from our range, leading to a HUGE POT if we actually connect the flush. This also allows us to check higher cards on the turn such as Js, Qs, Ks while allowing Vil to check behind with top pair if they did connect on the turn to see what our play would be on the river (turning thier hand into a bluff catcher). If thats the case, we river our flush. We bet huge after a checked turn. We force the LAG/NIT style players into a huge decision for most of their chips. Since the only real hands we would have at best is top 2Pair, or a (very rare set of Ts). When in reality we rivered our Nut flush, allowing for a huge payday. You might say, "But JB, Donking is bad. If we get raised, or called on the flop we don't know where we are at in the hand."
And I agree with that Statement 100%, but with how this flop came out. We need to find a way for Vil to hold on to some equity in the hand in case we do hit our flush. We have the A, if the flop goes check, check, and we turn the flush. We bet right? Unless it's an K or a Q Vil really has nothing in their range to call us with. if it goes down as describe, and we turn the flush. Chances are it goes check check on the turn, fold to river bet unless they happen to complete a straight. This allows Vil a chance at a free card if they check 2 pair, or a set on the turn in hopes for the board to pair on the river. We really don't want them seeing a free river, just in case they are drawing to a boat.
So with all that said, I don't mind not knowing exactly I am in this hand, on this flop after donk betting. There are a ton of cards that could be good for me, and only a few that could be very bad. but we could lose this hand if played passively, along with the Vil losing equity, and not calling if we do hit.
As played its an obvious check call. If you were willing to call this PF you needed to know you were looking for nothing less then a draw. You got that draw, now you have to play it strong. even if that means calling a 2/3 pot Flop bet. Something else that can be eliminated if we donk bet here.... Just something to think about.