Nevin-Wharton, who plays for the Sandiway club, defied the rest of the field to catch him by posting a superb total of 66.
His six under par round put him in clear, pole position to qualify for the next stage, final qualifying for the Championship proper, which takes place at Royal Birkdale in July.
Andy Palmer (Chorley) gave himself a fighting chance of getting through himself with a 69, a score shared by Adam Stone, of Lancaster.
By contrast it was a day of toil for Blackpool North Shore's Currtis Dean.
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He failed to register a score after losing a couple of balls during his round, played in warm conditions at the South Fylde venue.