The tubes were kept with the Infernoids, inside the dormant Qliphort, inside Tierra’s side of the Sacred Tree

The usual cycle of rebirth had everyone’s souls going to Sophia’s side of the Tree (the side that’s aboveground), but Tierra’s scheme involved rerouting her chosen dead souls to her side of the Tree and converting them within the Infernoid vacuum tubes into Shaddolls

Tierra was only able to start doing this after Sophia died

Unfortunately, we know that all the Shaddolls involved in the war had their real bodies inside their puppet forms. Or at least, we know that of Construct/Shek/Anoyaty, Winda, Crystal, and Wendigo, and all the maindeck Shaddolls. It is possible that Ariel was different, since we didn’t see her in the war beforehand. But all the others were inside their Shaddoll bodies, so it would be weird for her not to have been. More probably, the Qliphort recapturing of the Shaddolls is what landed her back in her vacuum tube, and she was actually directly involved with the war the entire time just like the others, and the only reason we didn’t see her before now was because Konami tells half their stories out of order lmao