No, he's still there. He's deep inside Gullet.

I think it's a one-time only battle inside the sigil. Once you defeated the skeletons and leave the house in Skull Island, you can't go back in again.

i did it and the sigil is no longer there for me too

I think this should be changed and revised to make it a bit more like a full-fledged longer adventure, with an instance quest of it's own, too, seeing as getting a magical Krokotopian lamp shouldn't have to be, well... that easy, in terms of enemy encounters and instance chambers and the length of that instance. I'm thinking that it should have a new hole dug underneath that homestead, leading to a new cave filled with new normal and boss enemies and some puzzles to solve or something, and where that Krokotopian lamp should be located at the end of the cave, complete with a new final boss enemy to fight at the end, preferably a corrupt Krokotopian Pharaoh spirit, accompanied with Krokotopian Mummies. If it helps to save time for the P101 team, they should be reusing similar design assets from Wizard101's Krokotopian enemies from that world, much like how MooShu uses many similar enemies and layout maps from that game, for example, even though some of it's locations and enemies are original. Picture this in your heads.

Also, I have to agree that it should be replayed and the sigil entry for that instance, the Abandoned Homestead, should remain available, because that instance being "one and done" thing after completing that quest, just brings nothing but little upset among Pirates.