Sir Thomas was asked to review expenses after the scandal
MPs will be allowed to appeal against repaying expenses judged to have been overclaimed, says a Commons committee.
Many MPs were angry that an audit of second home claims over five years imposed retrospective limits on claims for cleaning and gardening.
Gordon Brown was among those asked to repay money. He urged MPs to pay up but others planned to defy the demands.
The Members Estimate Committee warned MPs they would dock their pay if they lost appeals and did not repay money.
Auditor Sir Thomas Legg sent out letters to MPs with his initial recommendations that they repay money, or provide more details, in October and they have been responding to him.
Appeal court judge
His final letters to MPs will go out next week, on 7 December.
It is up to the Members Estimate Committee to decide what to do about Sir Thomas's final recommendations, expected in early 2010.
It has asked former Court of Appeal judge Sir Paul Kennedy - who was also the government's Interception of Communications Commissioner - to consider written submissions by some MPs.
It says they must show "cause why there are special reasons ... that it would not be fair and equitable to require repayment either at all, or at the level recommended".
The appeals process is expected to be completed by 15 January 2010, after which MPs will be asked to vote on the committee's recommendation that they pay back the sums requested.
Committee member Sir Stuart Bell said: "There can be no back-sliding. Those who do not pay back will have the sums deducted from their salaries or allowances."
But Labour MP John Mann told the BBC it suggested they were "overruling" Sir Thomas.
"MPs still don't get it, they remain out of tune with public feeling over this issue," he said.
"It's the same old story of the gentlemen's club unable to let go."
Sir Thomas was asked by Gordon Brown to review all past claims back to 2004 under the second homes allowance, following the scandal over MPs' expenses.
Sir Thomas has audited MPs' second-home expense claims made since 2004
But as well as checking claims were correctly made, he chose to impose retrospective limits, saying MPs should not have claimed more than £2,000 a year for cleaning and £1,000 a year for gardening. MPs were asked to pay back any claims over those limits.
Many were furious, pointing out that they were allowed under the rules at the time but Sir Thomas has said working out exactly what those rules were was "not straightforward".
There was also some annoyance that MPs with relatively small claims were being asked to repay money, while those who accrued large sums through selling on their taxpayer-funded second homes had not been.
Prime Minister Gordon Brown was asked to repay £12,415, largely for cleaning. He repaid the money immediately and urged other MPs to do the same.
Apology to Ken Clarke
Conservative leader David Cameron has said all Tory MPs will have to pay up at the end of the review or they will not be able to stand for the party again.
The highest sum known to have been requested is £63,250 from Tory MP Bernard Jenkin, who had rented a property from his sister-in-law and claimed it on expenses.
He said he had not been told that MPs were banned from renting from relatives in 2006 and the Fees Office knew about the arrangement, but has said he will repay whatever he is asked for at the end of the process.
But Sir Thomas has admitted some errors were made. Shadow business secretary Ken Clarke queried a request for a £4,733 and won an apology - the request was reduced to £1,345.
Labour MPs John Mann and Michael Clapham also queried smaller sums they were asked to repay and told they owed nothing.
A separate review of MPs' expenses recommended that they no longer be allowed to claim for mortgage interest on properties - or services like gardening and cleaning at all.
They are under consideration by the new body set up to run MPs' expenses.