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There's a fan theory I saw before about Wagahai's shackles. It says that they were placed there a long, long time ago by Council. They realized how much of a danger Wagahai posed to the universe at large and moved to stop her before it was too late. I personally like this lore and consider it to be true, even if it isn't official or anything.
The thing is that Council now lacks Sana. They lack the crucial element of Space. Without such a fundamental aspect of power, it is unlikely they would be able to reshackle Wagahai if she ever broke free from her power limiters. When the shackles break, the Age of Laplus will begin.