When the election is decided by under 2%, a targeted denial that is enough to swing the election is small enough that very few states would lose any representation at all in Congress.
Besides, it is hard to convince a government to apply section 2 if the party in power is the one that was doing the disenfranchising.
I could be wrong, but the Congress does not and would not execute the amendment's clauses. That is the executive's job. Thus it'd pretty much be the DOJ, I'd think, stepping up to make the threat, calling the states' attention to the fact that there are consequences set forth in the constitution they cannot fight against.
Besides, it is hard to convince a government to apply section 2 if the party in power is the one that was doing the disenfranchising.