Hundreds of pages of files relating to the inquiry into Nicola Sturgeon failed to appear on the Scottish Government's website after they were released last week.
A total of 18 batches of files amounting to thousands of documents were published on Tuesday.
However, on Friday the government re-released the documents following errors in the redaction process.
When it re-released the documents only 17 of the batches - which did not include the last batch - 18 - appeared on the website. Batch 18 included 234 pages of documents.
The 18th batch of documents was re published on Monday after what the Scottish Government said was a "glitch".
Re-issuing the files on Friday the Scottish Government said the documents had been re-issued because of errrors in the redaction process.
"FOI Decision 281 has been reissued following a small number of corrections in order to address certain minor errors in redactions, such as personal data," a note on the re-release documents stated on the Scottish Government's website.
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The Scottish Government has not said exactly what information was released which should not have been.
Both the files released on Tuesday and the re-released files on Friday were heavily redacted.
There are questions about why the government apparently released the identity of a civil servant who was seconded to the Hamilton probe in 2020/21 and who liaised between Mr Hamilton, a former director of public prosecutions in Ireland, and John Swinney. Her name was initially released but later redacted.
Mr Swinney was at time deputy First Minister to Ms Sturgeon.
The government last year said it would not provide this information because of data protection.
Its refusal followed demands for transparency and concerns by opposition politicians and Mr Salmond's allies that the inquiry could not have been fully independent if a Scottish Government official was working on the case and communicating regularly between Mr Hamilton and Mr Swinney.
In legal advice to ministers released in October 2024, senior lawyers also appeared critical of the set-up of the inquiry, casting doubt over claims that the probe was properly independent when the Scottish Government civil servant was so closely involved with the probe.
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Amid that controversy Mr Swinney told parliament it was normal practice for civil servants to be seconded to inquiries, and the civil servant working on the Hamilton inquiry had only dealt with practical matters.
The Conservatives and Labour both called for a judge-led public inquiry to be held into whether the inquiry was fully independent, but Mr Swinney said he had “absolutely no intention” of agreeing to that.
The release of documents last Tuesday was the biggest sets of files to be made public by the Scottish Government following a long-running freedom of information battle by the transparency campaigner Benjamin Harrop relating to the Hamilton probe.
Other evidence to his inquiry remains under wraps with the Scottish Government launching legal proceedings against the Scottish Information Commissioner in January to stop their release.
The correspondence made public last week sheds new light on behind-the-scenes tensions during one of the most politically sensitive investigations in recent Scottish history.
The Hamilton probe into Ms Sturgeon was triggered after the former First Minister referred herself for investigation following claims she failed to properly record meetings and discussions with Mr Salmond in 2018 after he had been accused of sexual harassment by two civil servants.
Mr Salmond had the exercise set aside in a judicial review with the Court of Session ruling it was "unlawful" and “tainted by apparent bias”. The court awarded Mr Salmond £512,000 for his legal bill.
A parliamentary inquiry was later set up to examine how the Scottish Government mishandled the probe.
Separately Mr Hamilton examined if Ms Sturgeon had breached the ministerial code.
Ms Sturgeon was ultimately cleared in his inquiry when he published his report in March 2021, though Mr Hamilton said she had given MSPs an “incomplete narrative of events” by failing to tell them about a key meeting, and it was only because he deemed it “a genuine failure of recollection” and “not deliberate” that it did not amount to a breach of the code.
Both the committee and Mr Hamilton's probe into Ms Sturgeon followed Mr Salmond's acquittal in March 2020 of 14 charges of alleged sexual offences.
Mr Salmond died aged 69 in October 2024 while attending a conference in North Macedonia.
In January last year, Deputy First Minister Kate Forbes refused to release the names of civil servants who had access to submissions made the Hamilton inquiry.
Her response followed questions from Fergus Ewing, an ally of Mr Salmond, for the names to be released to give transparency.
Mr Ewing said that the arrangement may have meant the government had influence over the probe and was able to get the investigation outcome it wanted.
Ms Forbes responded: “Several Scottish Government officials had permissions to access the mailbox used by Mr Hamilton’s secretariat.
“The reason they were granted access was for business continuity purposes, for example, if there were an urgent business requirement in the case of unexpected absence. The individuals who had permissions to access the mailbox were permanent civil servants. To comply with data protection principles the names of those civil servants are not disclosed.”
The Scottish Government said batch 18 had not been withdrawn but had not appeared on the website for a temporary period because of a "glitch".
The Herald was told no documents were withdrawn from publication.
The government said one group of FOI documents were not available on the Scottish Government website over the weekend "as the result of an administrative error" made "while minor updates were being made to the documents".
It added this evening that this was rectified earlier today. All batches of documents were reissued to the requester on Friday, it said.
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