It is unfortunate that the response from the Chief Magistrate's Office doesn't identify the authority on which he claims the right to intervene in what appear to be cases that have previously been decided.
So far as I can tell, the most likely basis for such intervention is by reference to Part 44 of the Criminal Procedure Rules 2020. That caters for the reopening of a limited range of cases in a magistrates court. Part 44 applies to cases where the defendant had not found out about the case prior to trial, to cases falling with Section 16M Magistrates Courts Act 1980 (defendant’s acceptance of online conviction option under Section 16H of the 1980 Act), and to cases covered by Section 142 of the 1980 Act.
Section 142 appears to offer the most likely basis for the Chief Magistrate's intervention. Under Section 142(1):
“A magistrates’ court may vary or rescind a sentence or other order imposed or made by it when dealing with an offender if it appears to the court to be in the interests of justice to do so; and it is hereby declared that this power extends to replacing a sentence or order which for any reason appears to be invalid by another which the court has power to impose or make.”
I note that this subsection only entitles a magistrates' court to vary or rescind a sentence or (like) order; it confers no power on the court to quash the conviction. However, Section 142(2) provides that :
“Where a person is convicted by a magistrates’ court and it subsequently appears to the court that it would be in the interests of justice that the case should be heard again by different justices, the court may, ... so direct.”
And Section 142(3) goes on to provide that:
“Where a court gives a direction under subsection (2) above—
(a) the conviction and any sentence or other order imposed or made in consequence thereof shall be of no effect; ...”
from which it is clear that the effect of a subsection (2) direction may be to set aside a conviction, pending re-consideration of the case by a differently constituted bench. That, however, amounts to nothing more than a temporary rolling back of the conviction, as it seems clear from the terms of subsection (2) that a direction given under it must lead to a rehearing of the case which may, or may not, result in an acquittal.
CPR Part 44 paragraph (7) indicates that a magistrates' court may exercise its power under Section 142 of the 1980 Act to set aside a conviction on its own initiative, whilst paragraph (8) goes on to set some constraints in the manner in which it may exercise that power, including an obligation before doing so to receive representations from an affected party (unless such party has agreed to the course the court is proposing to take or has itself proposed that course to the court). That may explain why the Chief Magistrate has invited the attendance of representatives of Northern Trains and Greater Anglia (though the latter has apparently chosen – as it may – to forego its opportunity to make representations). Since Northern Trains is represented by counsel, it is highly desirable for there to be 'equality of arms' in the form of professional representation of the six defendants, and if the Chief Magistrate has selected them as being representative of a wider class then the expense of such representaton should be underwritten by the state.
So far as I can see, even if the Chief Magistrate is exercising the power conferred by Section 142(2) (and it's hard to see what other power to intervene can be applicable), to quash convictions forming the subject of the six test cases, the limited effect of its exercise can be be nothing more than a rehearing of those six cases, and cannot of itself result in the quashing of up 75,000 convictions stemming from unauthorised use of the Single Justice Procedure.
In any event, the most damning aspect for me of the improper resort to the SJP is the supporting role it is likely to have played in deflection of appropriate magisterial scrutiny from the real mischief of seeking conviction for a Section 5(1) RoRA offence in cases (of which there may be thousands) where the accused could not properly have been convicted by reason of having given name and address in order to receive a penalty fare. In every case where that occurred there must surely be a prima facie case for enquiry into whether the prosecutor concerned failed to discharge his duty to make the court aware of a matter exculpating the accused, and where there is evidence that such a course of action was pursued on a systematic basis there must be grounds for wondering whether this amounts to a perversion of the course of justice. I hope that the reported review by the Ministry of Justice, HM Courts & Tribunal Service and Department of Transport will be taking steps to establish whether any such systematic abuse of a prosecutor's obligations has taken place, and, if it has, proceeding appropriately against the responsible parties.
Finally, if Northern Trains wishes to persist in its absurd argument that Section 5(1) RoRA creates a substantive offence of ticketless travel, perhaps it should be encouraged, on conclusion of the six test cases, to seek a determinative adjudication of the point by way of case stated.