The Haitians that were killed were in situ, the ones that washed ashore in San Pedro were the Dominican victims of the dictatorship who disappeared and their bodies were never found again (including some foreigners such as Jesús de Galíndez who was a Spaniard and whose remains were never found after he was kidnapped in NYC and taken to SD to be tortured and killed for writing a manuscript on the Trujillo dictatorship).
There are reports and news articles from the era where it becomes clear by simply putting attention to the details of certain things. For exampke, the complaints and increase of Haitians running away from the massacre was exclusively on the northern border. That was the main reason the Haitian government sent a delegation to that part of the border only to investigate. Several hospitals in northern Haiti from Juana Méndez to Cap Haitian received many injured. Outside of that area of Haiti not one hospital received any injured. The Haitian government itself gave a much smaller estimate of the total victims that was less than 5,000 (don't remember the exact figure) until the USA got involved and pushed for the Dominican government to indemnicize the victims via the Haitian government. From that point forward their "estimates" increased since the indemnizarion was on a per head basis. While the Dominican government did paid an indemnization to the Haitian government, there is no evidence any of that money were given by the Haitian government to the families affected. Plus, the actual figure is much greater than is typically cited, because that figure is of dollars at that time and not taking into account what that qmount would be in today's dollars,
There is no evidence at all that San Pedro was anywhere near the northern border or that any Haitian was taken to SD or elsewhere.
As said previously, human remains are discovered on a yearly basis in the DR such as the discovery of a burial site in Samana or a few years ago of another burial site in Moca. They send samples to institutions abroad, usually to the USA or Europe, to analyzed things such as Carbon-14 to have an estimate of how old they srr snd other aspects of the DNA to know from where they likely were from (in the Moca discovery not only was that from colonial times, but the discovered a hodt of places of origins of the remains including Great Britain which shocked many people.) It's a mystery they haven't found a single one pointing either to that time or origins in Haiti. The logical explanation is that there has been muchh exageration regarding this for political issues. You can't find what isn't there.