Autonomy has taken some of the blame for last quarter's disappointing performance at HP's software division, which fell short of HP's expectations.
Whitman said in an email ahead of speaking to staff yesterday that it was "always hard when a charismatic founder, who has built a great company leaves."
But Autonomy staff had a "very bright future" aft HP, she said. "While this will be a journey, I am confident we can do it together and I am committed to your success."
The Silicon Valley giant has stressed that Lynch's departure was down to the division's poor performance rather than the notion that Autonomy had no place in HP's corporate culture.
"There was a miss on the numbers," a HP spokesman said. "There's a discipline about financial responsibility for senior leaders in any organization. It was about bringing the executional skills to the business."
Some 15 to 20 percent of employees, about 250 people, had already left Autonomy since the deal was announced last August, including the chief financial, marketing and operations officers, said an Autonomy executive, who declined to be named.
Lynch, who had previously said Autonomy had a bright future within HP, will be replaced by HP's chief strategy officer Bill Veghte.
It is difficult to break out Autonomy's contribution to HP, but HP's software division revenue of $970 million in the second quarter of this year was lower than combined revenue of HP's division and Autonomy's a year ago.
HP said there had been a slowdown, although it was not an like-for-like comparison due to U.S. accounting rules, different revenue recognition timeframes and the shift to cloud computing, which delivered revenue over a longer period.
The Autonomy executive said it was not clear whether the shortfall was in the legacy HP products or in Autonomy products.
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