Holden, with his Saddlers contract coming to an end, had been invited back for pre-season after a year blighted by injury.
The Northern Irishman, however, is understood to have declined that offer and is instead working with Vale as he bids to return to full fitness soon.
Holden has a good relationship with Vale chief Clarke, who managed the player at Bescot.
Clarke technically signed the 24-year-old twice for Walsall having snapped him up on loan from Bristol City before making the move permanent in the summer of 2020.
Holden played 62 times for the club but has been dealt a series of setbacks over the past 18 months.
Having originally picked up a knee injury in December 2020, he has since undergone two surgeries and did not play a competitive game throughout the 2021/22 season.
His last official appearance for the Saddlers was in a 1-0 victory over Tranmere Rovers on April 13, 2021.
Vale are believed to have offered Holden medical help – funding specialist assistance among other measures – as he makes a gradual recovery from his long-term absence. Walsall had also taken Holden to see specialists during his time with the club.
It is thought Holden is currently undertaking running drills with the League One side while hoping to win a contract and be back playing games within the next few months.
The Saddlers may need to seek reinforcements in the attacking midfield area, although they did recently sign Isaac Hutchinson from Derby County while Jack Earing can also operate further forward.