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Daryl McMahon stood by his decision to change a winning side after Ebbsfleet lost at home to Sutton.
Fleet beat Hartlepool 1-0 on Saturday but the manager mixed things up at Stonebridge Road.
Ebou Adams, Myles Weston and Darren McQueen were all left out with Dave Winfield, Corey Whitely and Michael Cheek preferred.
All three players came off the bench in the second half but the U's took maximum points after punishing a defensive error.
"We’ve been here before on a Tuesday night after a game on a Saturday," McMahon said. "You change it, it’s the wrong decision, you keep it the same and you lose, it’s the wrong decision - you should have freshened it up.
"We’ve got 14 games in eight weeks and with the squad we’ve got, with how they train and how they work, I’ve got to use them.
"That’s why they’re at the football club. They’re all good players."
Ebbsfleet had plenty of possession but only forced one save from Sutton keeper Jamie Butler all night.
McMahon said: "I thought we moved the ball all right, through midfield into Corey and Keds. I don’t think that was a problem for us.
"As the game went on longer, they were defending their 18-yard box so there was no space and we were getting it wide and trying to cross because that’s all you can do. You’re hoping someone picks up a second and gets us a goal.
"I want us to be better in the final third but the general performance was good again.
"If we score first, we bring them out a little bit more. We did enough to score.
"In that first half-an-hour, you tell me, you watched the game. Who was the better side? Who created the chances? Who moved the ball? Who got into the box?
"We had good chances and I don’t mean a 25-yard shot, I mean a header from six yards out, a few of them, and at the end again.
"Sutton would have enjoyed the result but probably not the game.
"Paul Doswell (their manager) said after the game we should have won, they didn’t deserve that, but that’s no good to me because we haven’t got any points."