The back-and-forth in the comments is due to the fact that you are conflating the Gibbs paradox with the entropy of mixing - two distinct (albeit related) concepts. The former is specifically a quasi-paradox which arises in statistical mechanics, and so asking for its resolution in the context of thermodynamics does not make sense.
The answer to the question in the body of your post is that there simply is no discrepancy to resolve. Mixing two different gases is manifestly different from mixing two samples of the same gas; the former introduces entropy, and the latter does not. This is tied to the fact that the latter is reversible by simply re-introducing the partition, while the former is not.
One then might ask, what do we mean by different? Or rather, how different must two gases be in order for this "entropy of mixing" to take effect? For instance, I might say that I have two boxes of N$_2$ at the same temperature and pressure, so when I remove the partition between them, the entropy of the system stays the same. But you might counter with the fact that nitrogen has several stable isotopes - perhaps one box has slightly more $^{15}$N than the other. In the limiting case, perhaps one box contains pure $^{15}$N and the other pure $^{14}$N. At what point are they sufficiently different to conclude that an entropy increase has occurred?
The answer to that is an often overlooked subtlety in thermodynamics - namely that entropy is, to some extent, subjective. Let's say that Alice and Bob are physicists who study completely identical systems, but their experimental capabilities are different. Alice has a brand new dual-comb spectrometer which can precisely measure the ratio of $^{15}$N to $^{14}$N in her systems, but Bob's lab has not yet invested in that instrument. As a result, when Alice does her calculations, she treats $^{14}$N and $^{15}$N as different atoms, while Bob treats them as the same because he cannot experimentally resolve the difference with the tools available to him.
If Alice receives a box of $^{14}$N and a box of $^{15}$N at the same temperature and pressure, then she would be able to tell the difference between them. If she allowed the boxes to mix, she would say that the total system has increased in entropy as per the standard formula. The results of her experiments would be compatible with the predictions she obtains from her thermodynamic calculations.
If Bob received the same boxes, he would not be able to make the same determination. To him, they are the same gas, and when he allows them to mix, he would say that no entropy increase has occurred. And as long as none of his experiments are sensitive to the difference between $^{14}$N and $^{15}$N, the predictions he makes using thermodynamics would match his observations, too.
This all comes down to the question of how you define a "system" in thermodynamics - and the operational answer is that two systems are different if and only if you have the experimental means to distinguish between the two. The fact that thermodynamics is somewhat agnostic to fundamental questions of e.g. identity is part of why it is so powerful and general a framework.