Work had resumed at first light on Saturday, with one of the most powerful maritime cranes in Europe used to haul the 56-metre-long Bayesian from beneath the waves.
The Bayesian's upper decks appeared badly damaged while the blue hull was encrusted with mud after it had lain on the seabed at a depth of 50 metres.
Italian authorities in the nearby port of Termini Imerese will have a chance to inspect the luxury yacht next week as they seek clues into a tragedy that has puzzled maritime experts.
The Bayesian was moored off the small port of Porticello, near Palermo, in August last year when it sank during a sudden storm.
The yacht was vulnerable to violent winds and was probably knocked over by gusts of more than 117 km/h, an interim United Kingdom report said last month.
The salvage team, led by UK company TMC Marine, pumped sea water out of the hull and the vessel was held in an elevated position, surrounded by pollution containment booms, while further checks were carried out.
"This was a complex and precise lifting operation to recover Bayesian, and followed a step-by-step program of salvage work," said Marcus Cave, a director of TMC Marine.
The plan is for the yacht to be carried to port on Sunday before it is lifted on Monday on to a specially manufactured steel cradle on the quayside.
The recovery process has been made easier after the vessel's 72-metre mast was detached using a remote-controlled cutting tool and placed on the seabed on Tuesday.
In addition to Lynch, founder of the software company Autonomy, his daughter Hannah, lawyer Chris Morvillo and his wife Neda, banker Jonathan Bloomer and his wife Judy, and chef Recaldo Thomas were killed when the yacht sank.
Nine other crew members and six guests were rescued.
