The left-back was forced off after 26 minutes against Burton with a hamstring injury and replaced by Daniels, who proceeded to grab the Blues’ consolation in Saturday’s 2-1 defeat.
Worryingly, the same problem has kept Brown out of Pompey’s side on two previous occasions this term.
To make matters worse for Cowley, Michael Jacobs has been ruled out of the season through medial knee ligament damage sustained at Wigan.
The Blues’ head coach is now waiting to learn the full extent of Brown’s injury – but it opens the door for Daniels at left-back.
Cowley said: ‘Charlie is a really experienced player, he’s had a fantastic career and is very good for the younger players.
‘He got stronger against Burton as the game went on.
‘Charlie’s a great character, he’s obviously had a brilliant experience coming through the divisions with Bournemouth under some brilliant coaching from Eddie Howe, who is somebody we know well.
‘We came in on the Friday, Lee was already in the team and we didn’t make too many changes. The side has obviously won and Lee has done the job for the team.
‘There’s a real opportunity for Charlie. He’s going to have to dust himself down – he played 64 minutes and must be ready to go again.’
As for Brown, in November he pulled his hamstring while warming up ahead of kick-off at Lincoln.
There was a recurrence the following month against Ipswich – now it has struck again.
Cowley added: ‘It’s too early to say how long he’ll be out for, I don’t think it’s a bad one. I’m hoping it’s just a twinge, time will tell.
‘Having looked at Lee and the way that he moves, I think there's work we can do in his conditioning, such as mobilising his lower back to hopefully avoid them in the long-term.
‘Certainly for us it’s understanding how they move, looking at the injuries they might be susceptible to, and then putting conditioning in place so we are proactive.’
A message from the Editor, Mark Waldron
The News has launched a subscription offer which gives you unlimited access to all of our Pompey coverage, starting at less than 14p a day.
You can subscribe here to get the latest news from Fratton Park - and to support our local team of expert Pompey writers.