Schaeffer went top of the leaderboard after claiming four birdies on the front nine and then an eagle on the 12th.
Although she bogeyed the 13th she picked up three shots in a row from the 16th for her career-best round in five years on the Ladies European Tour.
Schaeffer finished the day on 11 under with Czech rookie Klara Spilkova holding a share of second place after a round of 70.
Spilkova is tied with German Caroline Masson who shot 69.
Schaeffer had wrist surgery in January but was back on tour in May and rediscovered her putting stroke at the Albatross Golf Resort in the Czech Republic.
She said: "I'm so happy because my putting is back and last week I played the same game but the putting did not rendezvous."
Sixteen-year-old Spilkova, from Prague, carded four birdies and two bogeys, but made some impressive putts to save par.
Sweden's Linda Wessberg and England's Kiran Matharu both shot 69 to end six under, with seven players a stroke further behind.
They were Cassandra Kirkland (69), Beth Allen (69), Louise Stahle (70), Becky Brewerton (70), Laura Davies (69), Anja Monke (70) and Felicity Johnson (71).
Julie Greciet of France recorded her first hole in one in an LET tournament with a six-iron to the third, her 12th hole of the day.
She ended with a second round of 71 to finish the day at four under.