Hendrie joined Pools for a second time in his career in the summer after leaving Grimsby Town but has been unable to force his way into a regular starting role at the Suit Direct Stadium under both Lee and previous manager Dave Challinor.
The former Burnley defender made just 11 appearances in all competitions this season, with seven of those coming in League Two.
It led to the 27-year-old raising concerns with the Pools boss as to where his future should lie with Hendrie keen to seek more first team opportunities.
Hartlepool United complete the signing of ex-Birmingham City and Walsall man
Paul Hartley addresses Hartlepool United links with ex-Celtic and Wolverhampton Wanderers striker
Middlesbrough secure loan-deal for former Leeds United and West Brom midfielder
How Hartlepool United were rated in Northampton Town defeat as ex-Charlton Athletic striker gets off the mark
Paul Hartley hints at possible transfer breakthrough for Hartlepool United
Lee handed Hendrie the captain’s armband in last week’s EFL Trophy quarter-final tie with Charlton Athletic, and helping Pools into the last four of the competition would be Hendrie’s parting shot with the club after negotiating the end of his contract on transfer deadline day.
“I’ve had many chats with Luke, he’s a fantastic professional,” explained Lee.
“He does everything right in training and unfortunately hasn’t had as many games under me as he would have liked.
“But because of the type of professional that he is, I've always been honest with him and spoken to him many times regarding his future.
“He had a couple of offers a couple of weeks ago and I said to him I wanted the decision to be his decision, I wasn’t going to force him anywhere.
“I was happy for him to be part of the squad and be patient. He rang me and said he didn’t know where he wanted to go with things and asked could he walk away from his contract?
“The discussions I had with him were just to make sure he was making the right decision, at the time he didn’t tell me he had anything else lined up, and the option was still here with us.
“We weren’t asking him to leave.”
Hendrie was released from his contract on deadline day and would later return to Bradford City where he spent half a season on-loan from Burnley during the 2017-18 campaign.
“I pride myself on setting high standards every day, being a good professional and giving it my all,” Hendrie said of his switch to Bradford.
“I am coming back a more mature person and have been given a second bite of the cherry which I hope to enjoy.
“I have only ever wanted to be successful in my career. If it is to be here, that would be very special.”
In light of Hendrie’s impending exit, Pools had been linked with a move for Oldham Athletic defender Carl Piergianni early on transfer deadline day with the Latics said to have rejected an approach for the 29-year-old.
It means Lee may be a man short in defence moving into the second half of the season, but the Pools boss was pleased Hendrie was able to secure his future elsewhere.
“He said he wanted to leave and cancel his contract so, because of the professional he is, we agreed to do that,” said Lee.
“But look, even if he’d have asked me about the Bradford deal I’d have still allowed it because of the type of person he is, so I’m delighted he’s got himself sorted.”