Louis Thompson and Michael Jacobs found themselves among Pompey’s substitutes on Tuesday night, despite featuring in the weekend win against AFC Wimbledon.
For Jacobs, in particular, it represented a surprise omission considering his pivotal role in that 2-1 victory, including netting the Blues’ equaliser.
Both were eventually utilised from the bench in the second half of the impressive 3-0 triumph at Sincil Bank.
And Cowley moved to clarify the reasons behind the pair’s removal from his starting XI.
He told The News: ‘Listen, I don’t want to be the Tinkerman, but I have to intelligently rotate.
‘It’s just where they are physically and Louis at the moment is probably two games a week, not three.
‘I wanted to play Michael (at Lincoln), I really wanted to play him, but I just felt holding him back would probably be the right thing to do.
‘If you haven’t played and then go back-to-back games – and with his history of injuries – it just felt like the sensible thing to do.
‘Your heart wants to keep it going, but you need to have this real discipline. No-one understands!
‘I can't break him, I haven’t got a big enough squad, so I must be really patient.
‘You want to pick your best team and the players that are in a good moment, but we are in a 46-game season, which is such an intense and busy schedule.
‘It’s no reflection on their performances against Wimbledon, it’s a squad game and everyone has to contribute.
‘When you are as small as we are in terms of the numbers, then we have to keep everybody going.’
Thompson had previously started three consecutive matches for Pompey, totalling 14 appearances so far this term.
As for Jacobs, Saturday marked his first League One start since April after an injury absence and, later, non-selection.
Cowley added: ‘They understand my decision, you communicate it well.
‘For me, it doesn't matter if you start or you finish. Sometimes the finishes are more important than the starts.’
A message from the Editor, Mark Waldron
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