I think when villain checks on this flop he either has the nuts (KdQd or maybe Kd9d?) or nothing (he'd probably bet Kdx -like KKd or AKd- or Qdx - like QQd or AQd). So when he raises you OTT, I don't think he is semi-bluffing or value betting worse (a little FD like 97dd would have bet OTF and there is no more 87dd, J9dd, T9dd, T8dd, etc.). Since the likelihood that you both have flushes are small, I'd do the same than you did in game but I'm wondering if we are not here in a spot where we can reduce villain's range to one hand (KdQd) and overfold (bet/fold) OTT.

"Wouldn't he reshove his whole stack as squeeze with KQd?" I don't know (because I don't know his tendencies) , You were at his table not me :p. Like I said above, I didn't see Q4d on his range. For me it was KQd or K9d. But with his line, I think you are very (very) often behind so you can bet/fold OTT (you block a lot a small flushes with your hand).