Flores explained his decision during a press conference for Espaynol today.
"I belong to Espanyol, I have contract and am honest with the club".
"I am the coach of Espanyol and will continue to be", Flores said. I am well and quite happy with my situation.
'There is nothing to tell.
"Football brings these types of situations".
"It happened three weeks ago with Gerard Moreno, but we have to think that we are happy with Espanyol".
On Wednesday, the Potters sent a delegation to Barcelona to meet Flores in the hope of securing a deal.
Former Ireland manager Mick McCarthy is the favourite to take over as the next boss should O'Neill depart for Stoke.
The club were willing to pay £1.7million to release No 1 target Gary Rowett from his contract with Derby, but the former Birmingham manager instead signed a new deal with the high-flying Championship side.
Stoke sacked Hughes last week following their humiliating FA Cup defeat at Coventry and Eddie Niedzwiecki has been in temporary charge since, taking training ahead of Monday's Premier League clash with Manchester United at Old Trafford. The Potters, who now sit 18th in the Premier League table, face Manchester United on Monday night.