Alonso's problems started when he ran wide onto the gravel at the final corner as he started his first lap in Q1 in Barcelona.
He recovered to get out of that session in 12th and then took eighth in Q2. With the car in a better state for Q3, Alonso believed he could still have made the front row, but a mistake on his final lap consigned him to ninth.
The team managed to gradually repair the floor during the gaps between sessions, but Alonso faced the additional challenge of not knowing quite how the car would behave each time he went out.
He has subsequently gained a grid spot from a penalty for Pierre Gasly.
"It was opening the first lap in Q1," said performance director Tom McCullough. "And he had a snap on the way in, whether it was a little damp patch, or probably pushing a bit hard. So it was just more of a low grip snap, the track not quite in good enough condition.
"When you fly into the gravel trap at that speed, it's just like sandblasting the car and the underneath, the strakes and everything got a real beating.
"It ripped off some of the vanes and winglets underneath as well. So yeah, we were definitely quite sub-optimal with the car."
While the crew in the garage tried to improve the car for each session engineers back at the team's base monitored the changing balance.
"The first run through the gravel trap did a lot of damage," said McCullough. "We were able to each time the car was in the garage repair the car, and actually slowly improve the car to the point that near the end of qualifying, we'd nearly got half of the deficit back from the data side of things.
"And also, we have a group of people monitoring the data back at Mission Control able to tell us the overall load loss and aero balance loss as we're evolving through the sessions, which makes it really good for the race engineers to be able to adapt the flap angle and try to get a balance on the car."
McCullough stressed that despite that flow of information, it wasn't easy for Alonso to adjust to a car that was changing each time he drove it.
"I think the Q1 damage in particular was really big," he noted. "So the fact that he made it through that was good.
"What was a little bit hard for him is every run we were repairing the car, we didn't actually know how much better it was going to be aerodynamically, and therefore the aero balance, until we'd actually run the car and got the data.
"So he was having to adapt. And he's very good at that. So he did a really good job there."
Regarding the crucial Q3 lap, he added: "Unfortunately, Fernando then in the end on his one new set of tyres in Q3 went in a bit deep to Turn 10 and ran wide on to the damp patch."
