Papers and communications seen by the FT reveal further detail on a second type of disputed transaction.
These involved sales of software Autonomy had made to resellers, intermediaries who hope to sell it on to end customers. The international accounting rules that governed its books allowed it to count sales to resellers even when no end customer was in sight – but only if the sale was final and there was no comeback if the reseller itself was left holding the bag.
According to papers seen by the FT, the way Autonomy should account for deals like these were discussed in emails involving HP executives after the acquisition, and before the whistle blower is said to have come forward.
In February 2012, for instance, an exchange of emails that included an HP executive concluded that one such deal, for $10.2m, should be shown as "deferred sale". One person familiar with the situation said that exchanges like this only showed that HP was making adjustments to Autonomy's approach to reflect US accounting rules.
Two large deals, extensive details of which have been reviewed by the FT, get to the heart of the dispute, and show how difficult it will be for investigators looking into the allegations to untangle the complex webs of transactions to determine their ultimate purpose.
(Read more: Autonomy made 'willful effort to mislead' HP: CEO Whitman)
One, booked in September 2010, involved the US Veterans Administration. Just a month before, on August 25, Peter Menell, an Autonomy employee, had reacted with surprise at the suggestion that the company might be close to recording a sale to the VA. "Am I missing something on VA?" he wrote to Mr Hussain, Autonomy's chief financial officer, in an email seen by the FT. "Why is it even being considered for Q3?"
The agency had not even issued an RFP – or request for proposal, the starting point in a bidding process – and six consortiums of tech companies were likely to compete for the work, Mr Menell wrote. On the last day of its September quarter, Autonomy booked a $7m sale to a reseller named Filetek for the VA project.
One person familiar with the sale said it was unrelated to the deal that Mr Menell had written about a few weeks before, and was tied instead to a separate purchase by the VA of email software.
The manner in which Autonomy was paid by Filetek is also an area of contention. On 30 June the following year, Autonomy made a payment of about $1.6m to Filetek and received back a slightly smaller sum the same day. A two-way transaction also took place on 2 August, with Autonomy paying $7.5m to Filetek and receiving $6m.
Deals where software companies buy from each other are common, and Autonomy's auditors signed off on these as being arm's length transactions. A purchase order seen by the FT, and contained in Deloitte's audit of the June 2010 figures, records an $11.5m purchase by Autonomy of Filetek software for its own data centres.
(Read more: HP showed 'willful blindness' on autonomy: Chanos)
A second deal,involving a proposal by the Vatican to digitise its library, followed a similar pattern – prompting similar claims and counter-claims. On the last day of the quarter in March, 2010, Autonomy booked a sale of $11m to a reseller, Microtech, to cover software involved in the potential deal. The Vatican was eventually to pick a different software supplier.
Months later, in early 2011, Autonomy paid $9.6m to Microtech and received an identical payment back from the company, according to one person familiar with the investigation.
One person familiar with Autonomy's position said, however, that Microtech made two payments totalling $8.7m, separated by six months.
Autonomy maintained that its purchase from Microtech was entirely unrelated to the Vatican deal, according to papers seen by the FT, with Autonomy recording the money sent to Microtech as payment for a "technology innovation centre" which was used partly to sell Autonomy products.
Whether the UK company got value for money – or whether this was a scheme used to fund payments made back to Autonomy – is typical of the many convoluted questions investigators may now be untangling.