Detective Superintendent Alan Buchanan, 47, became senior investigating officer for Lynda Spence's disappearance on June 2 2011.
The 27-year-old was allegedly abducted, tortured and murdered by Colin Coats and Philip Wade, both 42, charges which they deny.
During their trial at the High Court in Glasgow, it has emerged that Ms Spence was recruited by the Scottish Crime and Drug Enforcement Agency on March 5 2011 as a "covert human intelligence source".
Mr Buchanan said he was made aware that Ms Spence was "a source under recruitment" on July 15 2011 but that police did not have any information that linked it to her disappearance.
"It didn't greatly affect the strategy (of the investigation)," he told the court.
Under cross-examination, Gary Allan QC, defending Wade, said: "I really struggle with the fact it is not relevant where you are dealing with a situation where someone has dropped off the face of the earth."
Prosecutors allege that Coats and Wade tortured Ms Spence at a flat in West Kilbride, Ayrshire, in a bid to extract financial information from her.
They are said to have cut off her thumb, severed her little finger, burned both her hands with an iron, and beat her with a golf club and crushed her toe.
The case continues.