The short version is the Letwin amendment made the main vote legally pointless.
The following vote was to be the one on the main motion, that is the original motion, as modified by the amendments which passed. The original motion was
That, in light of the new deal agreed with the European Union, which enables the
United Kingdom to respect the result of the referendum on its membership of the European Union and to leave the European Union on 31 October with a deal, and for
the purposes of section 1(1)(a) of the European Union (Withdrawal) (No. 2) Act 2019 and section 13(1)(b) of the European Union (Withdrawal) Act 2018, this House approves the negotiated withdrawal agreement titled Agreement on the withdrawal of the United Kingdom of Great Britain and Northern Ireland from the European Union and the European Atomic Energy Community and the framework for the future relationship titled Political Declaration setting out the framework for the future relationship between the European Union and the United Kingdom that the United Kingdom has concluded with the European Union under Article 50(2) of the Treaty on European Union, as well as a Declaration by Her Majesty’s Government of the United Kingdom of Great Britain and Northern Ireland concerning the operation of the Democratic consent in Northern Ireland provision of the Protocol on Ireland/Northern Ireland, copies of these three documents which were laid before this House on Saturday 19 October.
and passing this test would have voided the Benn Act, and triggered all the actions in the original Withdrawal Act, mean Brexit with a deal on the 31st October 2019.
The Letwin Amendment passed however. This modifies the original text thus
Line 3, leave out from “deal,” to end and add “this House has considered the matter but withholds approval unless and until implementing legislation is passed.”.
So now the motion basically says "We'll back the deal if we like the legislation which permits it". In particular, this means the Benn Act still applies, and Mr. Johnson is under a legal obligation to request a further extension to the negotiation period (until the 31st January) from the EU.
It appears the Tory leadership didn't see any value in holding this vote, and would rather attempt to muscle through a "deal or no deal" meaningful vote next week or later in the month.