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Bercow didn't rule it out of ever coming back, he just said it currently can't come back unchanged (for MV2 there had been big enough changes from the EU in the associated legal assurances to warrant a second attempt).
May could get her deal back in a number of ways (in order of increasing skullduggery):-
a) Get the EU to agree to some other changes to the associated legal assurances such that it would pass as being different enough to warrant a third vote. The EU might be up for this as it would help resolve some of the uncertainty. (The EU, despite saying they wouldn't make changes, will almost certainly make changes. They said they weren't making changes last time and then made some). It's unclear exactly how much and what has to change, which puts Bercow in a tricky position.
b) Have a vote in Parliament to change the conventions/rules/etc that two motions cannot be debated more than once in the same session. As Bercow himself said, if things don't change they just stay the same. Nothing procedurally wrong with this.
c) Prorogue Parliament so it is in a new session.
d) Some other as yet unknown loophole to force the motion onto the order papers with the same deal.
She's got to be pretty confident that the deal will pass (i.e. she's bunged enough money to the DUP/ERG MPs) otherwise she/it is completely fux0red.
Keep reading that if she gets a short extension, May will try to bring her deal back for a third time. Since that's been stopped by Bercow, why is it still on the cards? Are people predicting if she gets the extension, she'll use constitutional skullduggery to overrule Bercow, or is there some more conventional way of doing it?