An MP whose property deals are at the centre of a police probe had her consultancy services terminated by the pro-business group set up to campaign for independence.

Michelle Thomson's payments as Managing Director of Business for Scotland (BfS) were axed months before the referendum amid clashes with the body's chief executive, according to BfS emails obtained by this newspaper.

However, she was allowed to continue using the MD title and carry out media work in order to avoid damaging press coverage.

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Until last week, Thomson was the SNP MP for Edinburgh West and the party's business spokesperson at Westminster.

She withdrew from the party whip on Tuesday after it emerged her former solicitor had been struck off for his role in various property deals linked to her.

In one case, her former business partner Frank Gilbride bought a house from an elderly cancer patient for £64,000, and sold it to Thomson on the same day for £95,000. Thomson then received “cashback" from Gilbride of £28,181.80.

Thomson’s role in BfS, which she helped found in 2012 to make the pro-enterprise case for independence, is now under the spotlight.

A tranche of BfS board level emails from last year reveal the body’s purpose of explaining the economic case to voters was undermined by internal rows.

A key issue was that Thomson and board member Ivan McKee were overtly critical of chief executive Gordon MacIntyre-Kemp.

BfS had MacIntyre-Kemp as CEO and Thomson as MD, and was overseen by a board chaired by entrepreneur and Falklands War hero Tony Banks.

However, months after her appointment, BfS believed Macintyre-Kemp and Thomson were doing similar jobs and the latter was spending too much time on media.

A perception existed that Thomson and McKee were getting a disproportionate share of prized television slots by BfS press officer Alison Balharry.

The tensions came to a head in March when Banks emailed senior BfS figures with a quote from an anonymous board member: “I thought we were on the same side – if this were a company I would want out – too much fighting – not pulling in the same direction – impossible to be fully effective.”

Banks issued a unity plea: “As from today, I think people need to take a long hard look at themselves and their behaviours.

“Life is about compromises and we need to look at the big picture here and put all our egos to the side. There is far too much energy getting wasted on nonsense and we are losing effectiveness because of it.”

Two options were considered for Thomson: ask her to resign; or stop her MD consultancy payments of thousands of pounds a month, but allow her to use the title and do unpaid media appearances for BfS.

The latter option was chosen and she was presented to voters during the referendum campaign as ‘managing director’.

Banks made the decision clear in a brutal email to her and others in BfS: “The fact is BfS cannot afford to fund your position and we will not be funding the position going forward, even if we have funds.”

He added that SNP chief executive Peter Murrell – described as ‘PM’ in emails – believed there was duplication in the Macintyre-Kemp and Thomson roles: “There have been remarks made by PM regarding having the both of you and the fact both of you should have been fund raising over the last few months! He does not think that we need both of you.”

Macintyre-Kemp followed up with an email of his own to Thomson and others: “Just to be completely sure of no further misunderstandings please do not attend the office today or seek to hold a team meeting.”

He added that "you could keep the title MD as that would help with debates and media". Balharry was also replaced.

The restructuring angered Thomson and McKee, both of whom were critical of the chief executive and frustrated by their diminishing role in BfS.

But Thomson, despite having her paid services dispensed with, then informed board members she had pulled in a £5,000 donation.

Banks responded sarcastically to the news: “Well done Michelle! It just goes to show that it is never too late for Board members to assist with fundraising and it is nice to see that happen, at last...In true Tesco’s manner ‘every little helps’!”

Another row erupted over whether Macintyre-Kemp or the outgoing Balharry should liaise with broadcaster Lesley Riddoch on a project.

In an email, McKee blasted Macintyre-Kemp: “Sorry Gordon, what bit of ‘Lesley only wants to deal with Alison’ do you not understand? Lesley is a well connector [sic] serious player and her 1st 2nd and 3rd impression of BfS is of a chaotic shambles....”

McKee also criticised the decision to lose Balharry: “Gordon has taken that decision as CEO, and he will sink or swim based on how good a decision that was...I have asked Alison to continue to work with me directly on supporting my media work so we can maintain that effort.”

In an attempt to resist the changes, Thomson and McKee wanted to air their grievances at an April board meeting, but not enough members were around to make it a quorum.

In May, McKee queried whether the make-up of the board was complying with its Articles of Association and floated the idea of directly electing member directors.

In an email to the board, Banks agreed there were problems with governance, but pointed the finger at Thomson:

“Our governance, even though I thought MT had it covered, has been less than what it should be.”

Thomson hit back at Banks: “I should appreciate it in future if you desist from inflammatory and unprofessional emails such as below. Frankly, I expect better from the chair of a professional business organisation.”

Former SNP Minister Jim Mather, a widely respected Yes elder statesman, used the next board meeting to criticise McKee and Thomson. “Michelle was shaking," said one person in the room.

By August, with Yes trailing in the polls on the economy, Thomson complained about being the managing director in public but having no actual responsibilities.

In an email to senior BfS figures, she wrote: “I do feel insulted...and am fed up with being forced to carry the can for situations over which I have no control and yet, to the outside world, still bear the accountability for.”

Senior Yes figures believe the BfS internal problems must be part of a post-mortem on the overall campaign, especially if there is to be a second referendum.

“It is vital that whichever pro-business body campaigns for Yes is credible and united. That was not the case last time," one said.

A spokesperson for Thomson said: "Michelle was very proud of the work that BFS did throughout the Independence campaign. Like any organisation and political campaign there were areas of disagreement - but all were pushed to one side to focus on the much more important job of looking at the business and economic case for Independence and persuading business of the benefits of it. Any attempt to stir up division now can only be viewed as mischief making."

McKee did not respond.