Portsmouth boss: Wigan Athletic deserve their Championship status back
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Latics require a single point to confirm their promotion back to the Championship with a game to spare.
And they can secure the League One title if they better second-placed Rotherham's result at Sunderland.
It would put right the wrongs of two years ago, when Latics lost their place in the second tier after being deducted 12 points for being placed into administration by the club's former owners.
"I think anyone with football in their heart will be pleased to see what is happening and the success they are having this year," said Cowley.
"When you see what happened to them in the 2019/20 season when they went into administration and got relegated, that was a travesty, it should never happen in modern day football.
"I felt so sorry for their manager, their players and certainly their supporters.
"Last year was tough for them as well, but to see them now with new owners at the back end of last season, to invest heavily into the squad, you only have to look at the depth to their squad and the quality they have.
"There are lots of players there who are capable of doing well in the Championship, if and when they get promoted."
Former Pompey players Jack Whatmough and Tom Naylor have played key roles for Latics this term after moving north last summer.
Indeed, Whatmough was named in the League One 'Team of the Year' on Sunday night.
"Yes, well deserved," acknowledged Cowley. "Jack is a top centre half.
"Within three days of being here in March, we were trying to re-sign Jack, but it just wasn't possible."
Cowley admits he's not been surprised at how well Whatmough and Naylor have done at the DW.
"No, not surprised at all," he said. "Both Jack and Tom, we were sad to see them go.
"They are really consistent performers. I only worked with them for a short period of time, but they were really good players for this football club, even better people.
"And they have made significant contributions to Wigan Athletic Football Club, who sit top of this division."
Cowley reserved special praise for his Wigan counterpart Leam Richardson, who was named 'Manager of the Year' at the weekend.
"He has done a really good job," added the Pompey boss.
"It is one thing having the finances, it is another thing putting it all together.
"I think he has recruited intelligently. He has recruited a lot of very experienced players for the level.
"He has moulded it and I think he has been exceptional in everything he has done."