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Michelle Thomson, the SNP MP whose property deals were at the centre of a police probe had her consultancy services terminated by the business group set up to campaign for independence.

Amid clashes with the body’s chief executive her salary as managing director of Business for Scotland (BfS) was axed months before the referendum but she was permitted to continue using the MD title and to carry out media work to avoid damaging press coverage.

Thomson, who was the SNP MP for Edinburgh West and the party’s business spokesperson at Westminster was withheld the party whip after it emerged her former solicitor had been struck off for his role in property deals linked to her.

In one case, her former business partner Frank Gilbride bought a house from a 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.

A tranche of BfS board-level emails revealed 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.

The perception was that Thomson and McKee were being give 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 both of you and the fact both of you should have been fundraising over the last few months. He does not think we need both of you.”

MacIntyre-Kemp followed up with an email 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 MacIntyre-Kemp. But Thomson, despite having her paid services dispensed with, then informed board members she had pulled in a £5,000 donation.

Banks responded to the news: “Well done Michelle, it 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 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 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 if in future you desist from inflammatory and unprofessional emails. Frankly, I expect better from the chair of a professional business organisation.”

Former SNP Minister Jim Mather used the next board meeting to criticise McKee and Thomson. “Michelle was shaking,” said one person who was in the room.

By August, with Yes trailing in the polls on the economy, Thomson complained about being a 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 believed the BfS internal problems should be part of a post-mortem on the overall campaign, especially if there was to be a second referendum. One said: “It is vital that whichever pro-business body campaigns for Yes is credible and united. That was not the case.”

A Thomson spokesperson said: “Michelle was very proud of the work 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.”