Historians appear to be correct that there is no conclusive evidence of this minority group settling in Bohemia.
That being said, it is possible that a Bohemian would have met a sub-Saharan native. There were several African Christian Kingdoms during this time frame and they made their way on several occasions to Europe through Pilgrimages.
You have pilgrimage sites in Bohemia dating to that time:
The monks of Plasy built a court around the chapel where they worked. People started to visit the site from far and wide and Pope Urban III granted the chapel special indulgence for the pilgrims in 1186, which was confirmed by Innocent IV in 1250. It became the oldest pilgrimage site in Western Bohemia.
The deanery church in Most, which stood in the middle of the church yard near the road to Žatec, burned down in 1515, and only the eastern crypt and the inner peripheral brickwork of the western tower could be saved. (The foundation of this church is indicated in 1253 till 1257 and indirectly proven by a document of pope Bonifacio VIII from 1296. The construction was originally an early Gothic basilica of three naves.)
These sites aren't that close to Skalitz mind you. Unfortunately any records from these locations appear to have been lost/burnt along the way. There were African Pilgrims, particularly from Ethiopia, in Europe during these times and we have evidence that they made it to Pilgrimage sites in Northern Spain (and we can find records proving they made the pilgrimage to Spain)...
As a fascinating sidebar, however, we do know about a significant African presence in medieval Rome in the 15th century. Beginning in 1402, multiple Ethiopian embassies arrived throughout Europe (notably in Spain, France, and Italy). This contact was sustained—by the 1480s, the church of Santo Stefano degli Abissini was built/restored in Rome specifically for Ethiopians to use (one seventeenth century writer dates this donation as early as the 1160s!). This established a permanent, dedicated place of worship for visiting Ethiopians and the burgeoning Ethiopian community. We don’t know exactly how many came, nor do we know all of their names and stories. But the overall point that black Africans were present and accepted in medieval Europe—especially later medieval Europe—remains.
They were present in Rome for pilgrimages and Bohemia contains pilgrimage sites...I would be surprised to learn that they settled into communities, but it would be hard to completely negate their presence.