British broadcaster James Allen claimed McLaren's decision to drop Mercedes as its engine supplier after 2014, paving the way for Honda, gave Mercedes "a bargaining chip" to end former technical director Lowe's 'gardening leave'.
On his F1 blog, Allen said Mercedes is "very unhappy" about the turbo V6 data that could flow to Honda next year, "so it appears they have leveraged this situation to trigger the early release of Lowe".
But McLaren boss Martin Whitmarsh on Tuesday told reporters releasing Lowe six months early simply "seemed like the right thing to do".
Briton Lowe, 51, will start work at Brackley in two weeks.
"It's not related to the Honda deal," Whitmarsh insisted. "The Honda deal and the Mercedes deals had been done, so there was no pressure brought to bear.
"It was entirely our decision and we hope that it creates some goodwill. Paddy's a good guy."