The influential defender was forced off with a hamstring injury in the 60th minute of the crucial 2-1 victory over Cardiff.
Ironically, the Irishman scored what proved to be the winner, having headed home Josh Murphy’s corner in the 17th minute to put the hosts 2-0 up.
Callum O’Dowda pulled one back six minutes later, but John Mousinho’s men held firm to see out a huge win and climb into 18th position in the Championship.
Yet that joy was tempered by another set-back for Shaughnessy, who was marking his fourth game back after long-term calf problems.
Mousinho told The News: ‘Conor has felt his hamstring, we don’t have a prognosis on it now. Obviously we’re disappointed with that.
‘He’s spent such a long time in his rehab getting back to the position he’s in and having played the games he’s played. He played against Burnley, he got through the game at the weekend as well,
‘We are obviously not particularly pleased for Conor, but we’ll have to see what happens. If we can get a scan in on Wednesday, we’ll get one as soon as possible.
‘The scan is one thing, it gives us an indication of time that he’s out, but, more importantly, we’ll treat the player and see how he is.’
Hayden Matthews was introduced in the 60th minute for the injured Shaughnessy, playing alongside Rob Atkinson.
The Australian once more put in an assured performance in what was his fourth outing since joining from Sydney FC last month.
He is now in line to stand-in for Shaughnessy on Saturday, when the Blues travel to 16th-placed Oxford United (12.30pm).
And Mousinho was pleased with how Matthews fared after his entrance against Cardiff.
He added: ‘I actually thought Hayden came on and did really well there.
‘We’ll see how Conor’s hamstring settles down, scan him on Wednesday and then go from there.’
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