According to Skyrim, the Skeleton Key needs to be in the Twilight Sepulcher, and there are Nightingales to ensure that it stays that way.
According to Lore, the term "Nightingale" has existed dating back to the era of Jagar Tharn, specifically during the adventures of Barenziah.
Now, in Daggerfall all the way to Oblivion (IIRC), it's possible to obtain the Skeleton Key.
Does this mean that Nocturnal removed the key from Ebonmere and gave it to the Eternal Champion/Nerevarine/Champion of Cyrodiil, thereby closing the Ebonmere, rendering Skyrim's Thieves Guild to fend for itself?