I am not a conveyancer but surely the Deed has conveyed the equitable interest. The legal title to the overage money when it is paid needs no document. Meanwhile the beneficiary has an unconditional right to call for the transfer of the legal title or other essential further assurance.
As overage is a contractual right, a chose in action and not land, the correct transfer is a legal assignment under s136 LPA 1925, critically requiring notice to the debtor, who otherwise could obtain a good discharge by paying the original contracting party. The Deed itself may be converted into a legal assignment by such a notice. The sole remaining trustee should be competent to give it unless the trust instrument prevents that. The contract must not make the chose unassignable. If it does the sole trustee and any replacement or addition hold the chose and its sale proceeds on a bare trust for the beneficiary under the Deed which, as long as otherwise valid, is an effective equitable assignment.
Thank you Jack. This is pretty much the conclusion we had come to with our conveyancing department but it is comforting to have someone independent of us agrees.
If we have any issues with the Land Registry I will update the post for future reference.