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Hythe are still waiting for their first home win of the season following a 1-1 draw against Horsham.
Shaun Welford's header from a Taser Hassan cross gave Scott Porter's side the lead in Tuesday's Ryman League Division 1 South clash.
But Horsham looked comfortable in possession and equalised through Byron Napper before half-time.
Herne Bay were 2-0 winners at Merstham in an FA Trophy preliminary round replay.
Jamie O'Connell broke the deadlock on the stroke of half-time, with Ben Brown clinching Bay's progress on 82 minutes.
Alfie May scored a 10-minute hat-trick as Chatham reached the third round of the League Cup with a 4-1 home victory over Ramsgate.
Ian Pulman gave Rams the lead against his old club nine minutes into the second half.
May's treble (71, 73 and 81) turned the tie on its head before James Alderman completed the win with a late tap-in.