Survival was the order of the season for Watford, with this FA Cup semi‑final jaunt to Wembley merely a cherished, if ultimately disappointing, bonus. For Quique Sánchez Flores, though, the notion has been turned on its head. One of the principal plot‑lines for what is now left of Watford’s season will concern the survival of the manager. Flores might have helped the club to ensure their Premier League position for next season. His own is rather less certain.

Gino Pozzo, the Watford owner, was in the posh seats at the national stadium and he looked inscrutable whenever the cameras picked him out, even after Troy Deeney had used his strength and sheer determination to find the equaliser on 55 minutes. But Pozzo and his family are known to be alarmed at Watford’s downturn since the heights of the marvellous home win against Liverpool on 20 December, which had the club in seventh place. Since then, the team has won three and drawn four of 17 league matches.

Flores appears to have been guilty of getting his points in the wrong order. Had he started the season with three wins in 17 but rallied to 41 points and a comfortable position of 12th, he would surely be enjoying hearty congratulations. Trends, though, are a part of how the Pozzos assess things while there have also been concerns that Flores has allowed his players to become a little too comfortable.

This defeat would have done nothing for Flores’s cause. His team were well beaten and it was difficult to say with conviction that any of those in yellow had seized the occasion. Little went right for Watford, from the switch-off that led to Yannick Bolasie’s opening goal and set the tone for the afternoon to the serious knee injury that forced off Étienne Capoue on the half hour.

Deeney’s goal came against the run of play and although Watford caused a flutter or two in stoppage time, the writing was on the wall. Flores walked over to offer a word of congratulation to his Crystal Palace counterpart, Alan Pardew, with 30 seconds of the added five minutes remaining and, when the full-time whistle blew, he had the job of consoling his players. There was applause from him for the Watford fans in one half of the stadium before he had to face the media for his latest grilling.

The one on Friday had turned the issue of his job prospects into more of an issue. Asked whether he would remain in charge for next season, Flores replied by saying that his future was “completely happy” because he had an “amazing family” and, in general, a great life.

He talked about how he lived for the moment, was “very happy” at Watford and was highly focused on the semi-final. It was not the time, he said, to talk about himself while another quotation had stood out.

“What I know is that it is one month until the end of the season and I want to enjoy it.”

Flores skated around and dodged more questions here but, again, he could offer no assurances that he would fulfil the one-year option on his contract. The Spaniard is popular among the Watford support and there has been surprise at the unfolding situation, which has come to the fore during the past week. It would feel cut-throat if he were to leave.

On the other hand, the Pozzos want their model for success to be above any dependence on a manager. To them, the structure is king.

At times like these, it can feel as if the managers are almost interchangeable and a penny for the thoughts of Slavisa Jokanovic would be worth the investment. He departed at the end of last season, after guiding the club to automatic promotion from the Championship. He was Watford’s fourth manager of the campaign.

This was Flores’s first visit to Wembley and his determination to enjoy it was undermined by the early concession. Only Nathan Aké knew what he was doing when he went from being touch-tight on Bolasie to bolting for the near post – to where Yohan Cabaye’s corner was directed. Following Damien Delaney’s flick, Bolasie was all alone at the far post to head home. Costel Pantilimon’s leaping kung-fu kick, as he chased back across his line, was in vain.

Flores and his players had been thinking about this tie for some time and it is possible that the prospect of it – and the cup run in general – has been a factor in their poor league form. They did not do enough in an attacking sense, their efforts lacking cohesion and incisiveness, and it said much that one of their best moments came when Joel Ward, the Palace right-back, almost put through his own goal under no pressure.

Flores felt his hopes surge when Deeney got the better of Scott Dann on José Manuel Jurado’s corner and, as the Watford support went into raptures, the thought of a scarcely advertised comeback win flickered.

It was not to be and the quality of Connor Wickham’s headed winner would have been sufficient to illuminate any game, let alone one as stop-start as this.

Flores would speak of not wanting to “justify what has happened this season” – in other words, make the case for what he has achieved. The Pozzos will sit in judgment.