The sun or moon moving directly in front of one another is a physical thing, but an eclipse itself is a concept and not a physical thing. Also, magic has rules just like anything else, they're just different from standard natural rules.
There are people out there who can just kind of hand-wave stuff that doesn't add up, but I've always been a stickler for details when it comes to stories. More power to the people who don't let that sort of thing bug them, though.
The sun being blocked out by the sun and casting a shadow on the surface of Earth is a physical thing with defined dimensions that change over the time of it's duration.
That is an eclipse (noun) which is not a concept.
You can become so much better at something than another person to the point that they are ignored and no longer "seen" in this matter.
That is an eclipse (verb) which is a concept.
The part you can't wrap your head around, I'm guessing, is sealing a physical entity inside what amounts to a massive shadow.
Now magically sealing something inside a shadow that's a concept that would make any physicist's head implode. ; )
Think of it like this, do you know the technical details and physics of how quantum entanglement works.
Neither did Einstein who called it "spooky action at a distance".
In fact, Einstein and his colleagues though that the effect should be impossible, but it has been verified that the effects of quantum entanglement are real.
So for all intents and purposes it might as well be magic since it currently goes against our understanding of physics.
In short... that shit is voodoo and you have no choice but to accept the reality of it.
So in the world of Castlevania there is a way to seal things inside an eclipse, you have no choice but to accept it because you saw it's effect in that world by way of the game you interfaced that world with. :3
But if you still need to rationalize it in physics terms, then think of it like this:
Somehow the area of the shadow caused by the moon eclipsing the sun was turned into an event horizon for a wormhole connecting Earth to somewhere far away and the castle and the entire cliff it was sitting on were transported through this wormhole. : ()
Either way it's not a plot hole. ^V^