League One latest: Harris retains hope massive former Portsmouth favourite will commit future to Gillingham as one-time Blues, Hull and Peterborough target is told he's too good for League Two
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The Gills named the midfielder as one of nine departures in their end-of-season retained list.
Thompson featured 17 times for the club following his January arrival on a free transfer from Millwall.
However, his deal was only until the end of the 2021-22 campaign, allowing him to walk away following Gillingham’s relegation to League Two.
Harris said Thompson’s name was included in those being released because it had to be under the circumstances.
Yet he still hasn't given up hope of luring the former Fratton favourite back for a second spell, with the duo having a long track record of working together.
And he admitted, if he did, Thompson – who played 27 times for the Blues during the 2018-19 season – would be among the fourth tier’s best players.
‘I would never say there isn’t a chance of Ben Thompson working with me, he goes on the released list just because he has to,’ said former Lions boss Harris.
‘I want him to stay, he lives 15 minutes up the road, he has played for me for a long time and we have a close relationship.
‘Ben Thompson is a top, top player in League 1.
‘In my opinion he would be one of the top three players in League 2 next season. He knows there is a home for him at Gillingham Football Club.’
Harris also admitted he would love to keep central defender Jack Tucker at Priestfield.
The highly-rated 22-year-old was heavily linked with a move to Pompey last summer.
The Blues were reported at the time to have bid £200,000 for the Gillingham youth product, joining Celtic, Rangers, Hull, Peterborough, Reading and Brentford in pursuing the defender.
He remained at the Gills, though, making 50 appearances this season.
Tucker’s contract is up, however.
And while a new offer is on the table, Harris believes the centre-back will leave.
Harris added: ‘We made him a (contract) offer because we want to keep our compensation rights but I would like to keep him because he is a great player and a good character.
‘But we have to be realistic and say "is Jack Tucker better than League 2?” In my opinion he is.’