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From an information request and a response under the Freedom of Information (Scotland) Act, published on 25th Sep 2019:

Details of any briefings by civil servants or documents provided to ministers in 2017 or 2018 on the topic of a second independence referendum.

The single most common concern among 7 500 responses was:

Conduct of the poll. One of the most prevalent themes was concern about security and risk of electoral fraud. Respondents made suggestions about how they thought security arrangements could be tightened. There was a particular lack of confidence in postal voting. Respondents supported the proposal set out in the consultation paper requiring 100% checking of personal identifiers on all postal voting statements. There was also widespread agreement with the proposal in the consultation paper that the counting officer must not knowingly appoint or employ anyone who has been involved in campaigning during the referendum.

https://www.gov.scot/publications/foi-18-02260-appeal/

These anxieties derive from dramatic events at the time of the vote in 2014:

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In the Guardian on 22nd September:

By mid-afternoon on Monday the number of names on change.org had topped 87,000. “We the undersigned demand a re-vote of the Scottish referendum, counted by impartial international parties,” reads the petition, which goes on to cite “countless evidences of fraud” documented during Thursday’s poll on independence.

At 38degrees.org.uk, a second petition had more than 62,000 signatories. “Investigate the vote counting procedures,” it demands. “Allow an independent re-count of all votes.”

https://www.theguardian.com › politics › sep › scottish-referendum-vote-ri…

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Later that year, the Sunday Post reported new evidence:

There were hundreds of attempts to illegally influence the outcome of Scotland’s independence referendum, a damning new probe has found. The Sunday Post has learned “several hundred apparently fraudulent applications to register to vote were received” ahead of September’s historic vote.

The alarming disclosure is contained in a report by the officials who oversaw the voter registration process. It comes only weeks after an investigation by the Electoral Commission found “no evidence” of widespread fraud.

The report by the Scottish Assessors Association (SAA), which represents electoral registration officers (ERO), also revealed there had been “widespread misuse and abuse” of provisions which allowed more than 6,000 people to carry out emergency proxy votes.

The scale and the attendant risks inherent in postal voting were also explored in a BBC Scotland report at the time:

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Back in 2004, the elections watchdog said there was no evidence of widespread abuse of the system, but some politicians were extremely sceptical. Conservative MP Alan Duncan told parliament that all-postal voting left “massive scope for fraud and undue influence“, adding: “It is, at every turn, open to fiddles“.

In 2005, judge Richard Mawrey QC delivered a scathing assessment of the system, after ruling there had been “widespread fraud” in six Birmingham council seats won by Labour the previous year. He said the case reached levels, “that would disgrace a banana republic”. To this day, Mr Mawrey maintains postal voting is open to fraud on an “industrial scale”, but the Electoral Commission says it would not be proportionate to end postal voting altogether.

Just like in elections, many people in Scotland have registered to vote in the independence referendum by post. More than four million people get to vote on 18 September, and the number of people with a postal vote went up from 570,587 in March to 680,235, as of 15 August – an increase of about 20%.

https://www.bbc.co.uk › news › uk-scotland-scotland-politics-28741264

At the time and for years after, the Scottish Conservatives were associated with rumours of system abuse:

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No charges were ever made.