According to the article you shared:
In 2006, a coalition of alumni and supporters of Maryland’s HBCUs filed the lawsuit, contending that the state had underfunded its four historically black institutions and allowed traditionally white universities to duplicate programs offered at HBCUs, undermining their ability to attract students.
The court ruled in 2013 that the HBCUs were not underfunded compared to traditionally white institutions, but that program duplication had perpetuated segregation. Since then, the state and coalition have been working towards an agreement on how to resolve the issue.
I’m not sure what the underfunding ruling was based on (and whether it’s the same method of underfunding that the feds are looking at now) but, from my reading of teh article, the settlement was because of the state chose to duplicate HBCU programming at PWIs, undercutting the HBCUs ability to recruit students.
According to the letter to Maryland (soure):
From my reading of the article, they are only referencing a disparity for the U. of Maryland - Eastern Shore, a disparity of over $320 million for the time frame of 1987-2020.