The Power and Kangaroos couldn't get a deal done for the 20-year-old by the time the Gillette AFL Trade Period ended on Friday, despite Jacobs alerting his club of his desire leave more than two weeks ago.
Jacobs told the Power he wanted to return home to Melbourne to be closer to his family.
The first round draft pick was absent from Adelaide Airport on Saturday morning as the vast majority of the Power's list flew out to a training camp in Italy.
He won't join his teammates overseas and won't play in the club's November 3 exhibition game in London against the Western Bulldogs.
Hinkley said that while he didn't think Jacobs' reasons for wanting to go home would change, he hoped the young defender could "come to terms" with his situation and stay at Port.
"We talk to Ben and we try and understand where Ben's at with his decision and hopefully we've got an opportunity that Ben may still consider Port Adelaide as a chance to play his football next season," he said.
"We've got to work through that with Benny and we'd love nothing more for him to come back and be a part of the Port Adelaide Football Club, but his reasons for going home were family-based reasons so I don't think that'll change.
"He's got to come to terms with that and then understand whether he can make the decision to come back and be a part of Port because we'd welcome him back really easily."
While Jacobs will miss the Power's four-day camp at the Australian Institue of Sport's European base in Varese, Italy and the trip to London, Hinkley said it would be the perfect opportunity to get to know the rest of his players.
Labeling himself a 'relationships man', the newly appointed senior coach said he would get ample one-on-one time with the players as well as the coaches.
"I'm about relationships and building them and I think it's a great chance to start some of that," he said.
"I think that'll happen just naturally (talking one-on-one with players), we'll get opportunities to chat and even as of today, when you get [on] a plane for 14 hours there's a great opportunity to talk to some players.
"I've only been on board for a small amount of time and the players have obviously been on leave and a lot of the coaches have been away, so it's a great opportunity for us to get together and actually understand a little bit about each other."
The exhibition match in London will be the first time Hinkley watches the Power as senior coach.
He said he was looking forward to viewing the game from a new perspective.
"I'll be really interested from a distance, sitting back and actually having a watch of the players," he said.
"For the first time for me I'll really be watching Port Adelaide as my club and I haven't had that opportunity in the past."
Harry Thring is a reporter for AFL Media. Follow him on Twitter: @AFL_Harry.
