John Marquis is expected to return to training this week after struggling with a tendon issue.
And the Blues boss is upbeat Lee Brown and Reeco Hackett’s issues will improve, after impacting them at Gillingham.
Hackett played while less than fully fit at Priestfield, while Brown missed out after initially being named on the bench.
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Cowley is hopeful those issues will alleviate in the coming days, with a scan proving positive news for Marquis - allowing him to return this week.
Pompey are hoping captain Clark Robertson will step up his recovery from his hip injury this week, after speaking to his surgeon.
Liam Vincent and Ellis Harrison are now back in contention, with Paul Downing (calf) expected to follow suit today.
That leaves just Ryan Tunnicliffe (hamstring) and long-term absentee Jayden Reid (knee) sidelined.
Cowley said: ‘Lee’s got a stiff back.
‘He came in Wednesday and was fine and came in Friday, started training and it stiffened up for no apparent reason really.
‘We were hoping we would be able to get him through, with Reeco maybe they were both 70 per cent fit.
‘We decided to go with Reeco, because he was perhaps less of a risk. Portsmouth can do without losing any more defenders.
‘Credit to Reeco because he played well short of match fitness, and that’s what you need the boys to do.’
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