Among the four players dropped for Saturday’s dramatic 3-3 draw with the Cod Army, unquestionably the absence of Thompson drew the most attention.
Supporters criticised the omission of the ex-Swindon man to create the space for Joe Morrell’s first-team return following a three-match ban.
During the Welsh international’s absence, Thompson has thrived, totalling four successive starts.
But for Cowley, naming him in his side against Fleetwood was a ‘big risk’ he wasn’t prepared to take.
He told The News: ‘There were just a couple of small tactical tweaks, the bigger problem for us was we couldn’t quite risk losing Louis against Fleetwood after playing 90 minutes at Shrewsbury.
‘I thought that was a real loss to us, that was the bigger thing for me.
‘We are getting there with Louis, he played 90 minutes on Tuesday, which was a real positive.
‘We needed him at Shrewsbury against a team which we know are very good on the attacking transition.
‘If we had played him against Fleetwood, I don’t think we’d have been able to use him against Oxford.
‘I think it would have been a big risk playing him on Saturday, he was very tight and sore the previou Thursday.
‘On Friday he did a bit of training, but it would have been a risk.’
Thompson has totalled 25 appearances this season following his summer release by Norwich.
His sole goal was that 84th-minute winner at Shrewsbury on Tuesday evening.
And also finding themselves left out of Pompey’s side against Fleetwood were Mahlon Romeo, George Hirst and Aiden O’Brien.
Cowley added: ‘With the other boys, we’ve just got games coming so thick and fast with such a small group.
‘League One football, particularly after two away travels – even though we played just one game – takes a lot out of you physically.
‘We have to keep freshening up the front end of the pitch if we want to play the way we want, with energy and intensity.’
A message from the Editor, Mark Waldron
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