The 15-year-olds were expelled from their school in Surrey for making abusive phone calls - including death threats - to a PE teacher.
But an independent appeals panel ordered that they should be allowed back into the school, where teachers are refusing to have them in their lessons.
On Thursday the Education Secretary, Estelle Morris, got the local education authority to arrange a meeting with the parents to offer the boys alternative places.
These would probably be in a "referral unit" for disruptive pupils.
'Undeserved'
The meeting is scheduled for Friday morning - but the mother of one of the boys has told BBC News she will not accept the deal.
Grounds for panel's decision
procedural error in the case
threats out of character and would not have been carried out
importance of continuing boys' education.
She did not deny her son had made the calls - but said he had "served his time".
"I haven't gone through five months of hell with my family to now accept that my son will go to a referral unit," she said.
The boys' victim at Glyn Technology School in Epsom, teacher Steve Taverner, is off work due to stress.
They apparently turned on him after he disciplined them for throwing stones at windows.
He showed his union, the Association of Teachers and Lecturers (ATL), transcripts of the calls.
Abusive calls
In one call which had been intercepted by the police, the boys said: "You have five days to live".
Another allegedly said: "You are going to die soon. You are going to get stabbed in the back of the head."
Mr Taverner said he had been appalled at the boys' reinstatement.
"I'm shattered by the decision that is stopping me from going back to school and I'm under a lot of stress over what has happened," he said.
"At the moment I could not cope with going into school with these pupils still in school."
Teachers' ballot
The head teacher expelled them in June and the school's governors confirmed the decision.
But their parents lodged a further appeal and the appeals panel said the boys should be allowed back.
The boys returned to school this month - but teachers have refused to teach them.
They have been educated apart from other pupils by a supply teacher.
The staff are now voting formally on whether to continue to refuse to teach the boys.
The result of the ballot, being carried out by their unions, should be known on Friday or early next week.
The incident has turned the spotlight again on the powers schools have to exclude pupils.
Glyn Technology School's head teacher, Stuart Turner, said: "Expulsion is an act of last resort and a school never takes such a decision lightly, but we must be able to make schools a safe place for everyone.
"Appeal panels that reinstate to their schools these disruptive pupils are undermining a school's ability to govern itself."
For this reason, two years ago the government issued new guidance to appeal panels.
This said students who even threatened violence against a teacher or other pupils should "not normally be reinstated".
Call to scrap panels
Estelle Morris said only last week: "Teachers cannot teach if children are disruptive.
"One child threatening or abusing one teacher in one of our schools is one too many."
Her junior minister, Stephen Twigg, said she had intervened in the Surrey case to get things back to normal.
"We believe the appeal panel didn't get it right - we are supporting the head teacher and governors," he said.
New powers not being used
But ministers cannot overrule the panels.
This week the Conservative Party - which introduced appeal panels when in government - restated its policy of scrapping them.
Ms Morris gave herself new powers in the 2002 Education Act to change the way appeal panels operate - but she has not yet used them.
One change would see a majority of panel members being teachers or former teachers.
Another would stop expulsions being overturned on a procedural technicality.
Regulations implementing the changes are not expected before next January.