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Dover bowed out of the FA Trophy in the second round on Saturday when they were beaten after leading against Harrogate.
Visiting top scorer Jack Muldoon was the man who sent them packing, instantly cancelling out Inih Effiong's 14th minute strike before claiming the winner midway through the second half.
Goalkeeper Mitch Walker, one of Dover's better players on the day, had earlier kept out a fifth minute spot kick from Mark Beck in a frenetic opening.
Home boss Andy Hessenthaler made two changes to the side which had beaten Havant in Tuesday's replay with Walker and Effiong both recalled.
Lee Worgan and Kadell Daniel dropped to the bench where there was also a place for forward Tobi Sho-Silva, back in the squad for the first time early December.
Whites went into the game unbeaten in six at home while Harrogate were without a win in five games, but it was the visitors came out of the blocks flying.
Josh Falkingham and Lloyd Kerry had both already forced smart saves from Walker when they were awarded a penalty inside five minutes.
Young midfielder Joe Bedford clipped Mark Beck in the box, but the big Harrogate striker's spot kick was saved by Walker, who went away to his left but managed to stick out a trailing leg to block.
Dover had barely been out of their half when they went ahead from their first attack, in the 14th minute.
Anthony Jeffrey's corner was only cleared as far as Effiong, who chested the ball down before producing an excellent left-footed half-volley from 18 yards to claim his 10th goal of the season.
Harrogate's equaliser came almost straight from the start and after they had won a free kick 35 yards on the Dover right.
George Thomson's flighted ball was headed back across goal by Callum Howe and Muldoon volleyed home for his 11th of the campaign.
Harrogate continued to look slick going forward but Dover were dangerous from set pieces with visiting keeper James Belshaw looking less than commanding from one Jeffrey corner.
Shortly after Moussa Diarra headed over from a looping Mitch Brundle cross after which the game began to become less frantic.
Walker did well to race outside his area to hack clear from Muldoon, and then, after Stuart Lewis had appealed in vain for a penalty on 40 minutes Effiong had another good shooting chance but fired straight at Belshaw.
Whites replaced Bedford with Josh Passley at half-time and they had an early opportunity when Josh Debayo whipped a free kick over from the edge of the box.
Jeffrey then curled an effort wide and another straight at Belshaw, while in between those efforts Harrogate's Beck had a great chance eight yards out but misdirected his header across goal rather than at Walker.
Harrogate's Kerry had an even better sight of goal on 56 minutes when Ryan Fallowfield's low cross picked him out but he dragged his shot wide.
The visitors did however take the lead on 63 minutes when Muldoon timed his run superbly to turn home Thomson's cross at the near post.
Liam Kitching blazed over from another good chance for the visitors but chances began to dry up after that with Harrogate keen to hang on to what they had while Whites struggled to get any momentum going.
Dover: Walker, Nortey, Brundle, Diarra, Debayo (Lokko 70mins), Lewis, Bedford (Passley 46mins), Allen (Reason 70mins), Effiong, Pavey, Jeffrey; Subs:Daniel, Sho-Silva.
Harrogate: Belshaw, Muldoon (Knowles 78mins) Falkingham, Kerry, Emmett (Woods 88mins), Kitching, Howe, Thomson, Beck, Burrell, Fallowfield; Subs: Cracknell, Williams, Langmead.
Attendance: 463