It wasn’t clearly defined in the 3.5 ECS. The approach of 4E was to say that Masvirik’s servants are vessels for its power and that this physically transforms them — and that the colonists mistakenly assumed these were distinct species, whereas in fact they are corrupted. So the classic “Poison Dusk lizardfolk” weren’t pygmy lizardfolk, but rather corrupted kobolds—with Dungeon 185 noting that the kobolds of the region are the most vulnerable to the influence of the Cold Sun, thus driving that idea that most of the time, people encountering “The Poison Dusk” encounter these small scales. It goes on to note that with Masvirik’s dusk shard champions “Many are physically transformed so that they possess serpentine or draconic traits and specifically resemble a black dragon” — so Blackscale lizardfolk aren’t a SPECIES, but rather corrupted champions of Masvirik. As such, they largely aren’t encountered outside of the Poison Dusk and don’t play a distinct role in Q’barra separate from the Poison Dusk.
Source: Lightning Round: Q'barra
The blackscale lizardfolk, largest and strongest of their kind (Large lizardfolk, HD 4d8+8, resistance to acid 5), live in the jungles around Haka’torvhak. As the chosen warriors of the dragon Rhashaak, they bully and dominate the lesser lizardfolk. They are hostile to the common races.
Source: Eberron Campaign Setting
Blackscales claim that their dark coloration and facial features are proof of a blood connection to the dragons of Haka’torvhak, but little proof to this claim exists.
The jungles of Q’barra are home to three distinct species of lizardfolk—the blackscales, the Cold Sun Tribes, and the poison dusk. The blackscales are the largest of the three, and throughout the history they have used their size to dominate and intimidate their smaller kindred. They are the guardians of the sacred city of Haka’torvhak and the warriors of the dragon Rhashaak. They are proud and arrogant, and are usually extremely hostile toward humans who trespass into the deep jungles of Q’barra.
While their culture is quite primitive, the black scales have access to the vaults and arsenals of Haka’torvhak. High-ranking warriors or priests wear glittering jewels, and the weapons of the blackscales are often elaborately carved and decorated. The guardians of the sacred city may be equipped with better weapons, shields, or armor—possibly even magic relics from the deep vaults.
The blackscales typically live off the “tribute” they extract from the other tribes—offi cially, offerings made to the great dragon and its guardians. The dragon priests hold the ultimate authority within society but rarely use this power; in the absence of interference from a priest, the most powerful warrior rules the tribe. Any of the three species of lizardfolk can be called to serve as dragon priests; the blackscales consider the priests to be a fourth tribe, and thus see no shame in following their commands.
Source: Monster Manual III