Castlevania itself is a creature of darkness, so wouldn't sealing the Castle inside the eclipse be sealing the creature? It may be unable to change and shapeshift because of the seal. Just maybe sealing the VK inside also attributed to this.
Also, after the destruction of Dracula in 1999, is it necessary that Castlevania manifests when The Dark Lord's return is imminent? If so, during the events of DOS, there was still potential for Castlevania to return during these events, the point of luring Soma to Celia's fortress (the replica of Castlevania) was to awaken the Dark Lord.
Maybe because the original Castle is still sealed inside the eclipse it will rarely be seen again, but this would mean the new Dark Lord can still manifest regardless.