I read this paper: https://eprint.iacr.org/2016/197
It says that CTR and OFB modes are safe against quantum adversaries.
You have to understand the attack model that assumes. It assumes a scenario where the attacker can make quantum entangled queries to the Oracle, and get entangled responses back; what they show that, even in that scenario, the attacker does not have any significant advantage over just attacking the underlying block cipher itself [1].
Now, if what you have is disk encryption, and the 'queries' that the attacker is allowed to make is examining the ciphertext (which are made up of classical '0's and '1's), he has no opportunity in attempting such an attack, and so the paper is completely irrelevant to you.
I have an external HD fully encrypted with Threefish block cipher in CTR mode with 3 layers of 1024-bit keys.
And how do generate these keys? Unless you generate them completely randomly, and store them somewhere perfectly secure, you don't have nearly as much security as you think. For example, if you generate them based on a user-entered password, then you have no more security than what's in the password.
[1]: I feel the need to point out that this attack model feels extremely contrived; we literally do not know how to make an implementation that would allow such an attack.
