Stoke have been on the lookout for a new manager since getting rid of Mark Hughes last week and have been courting Espanyol head coach Flores.
"I'm not going to talk about me on such an important day for Espanyol", he told reporters after the match. "I want to continue being happy with my profession".
The 52-year-old is under contract with La Liga side Espanyol until 2019, but has a release clause in his deal.
Stoke have also spoken to former Leicester, Aston Villa, Celtic and Sunderland boss O'Neill.
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The Irishman also has a good relationship with club chairman Peter Coates, but there is a view around the club that O'Neill would be a more short-term appointment to maintain their status, while Flores' style is more what they are looking for in the long term.
"I'm very grateful to Espanyol, I've been frustrated sometimes because we haven't advanced as fast as desired, but that's because Espanyol haven't been able to, not because they haven't wanted to", he added.
Their attendance suggests the pair will in fact be staying on as Republic of Ireland manager and assistant manager after days of speculation linking them with a return to the Prmeier League.
But the 65-year-old said after the Republic lost their World Cup qualifying play-off the following month that he would need to have "a real think" about his future, and still nothing has been signed.