Mijares breezed past Niño Anthony Go, 21-13, 21-13, to arrange a duel in the round of 16 against Francis Rey Gomez of Corpus Christi School, a 21-9, 21-6 winner over Wyrlo Reyes.
Flores, on the other hand, booked a ticket to the next round after eking out a 21-15, 15-21, 21-14 victory over Martin Carbosa of University of the Visayas (UV).
He will meet Andre Mark Peroy, who won over Rocando Suico, also via a three- set thriller, 20-22, 21-17, 21-13.
Mijares and Flores will see each other if they can hurdle past their respective opponents in the round of 16.
Another top player Patrick Duarte of USJ-R is all by his lonesome in the other bracket as he led to the exit door Bryan Tanudra of UV, 21-15, 21-15.
He will next meet Fausto Berganting, who ended the bid of Steve Alda, 21-12, 21-13.
In the women's elite division, Hazel Blyth Peroy of University of Cebu (UC) and Kara Melanie Montejo of USJ-R are already in the quarterfinals having enjoyed a bye in the first round.
Peroy will meet next the winner over Moonyen Armecin of USJ-R and Lelia Tampon while Montejo is set to face either Rojane Lisondra or Leah Kathleen Garaden.
The JVC regional is sponsored by JVC, Victor (exclusively distributed by Pcome Industrial Sales), Lactacyd and Bingo Bonanza and backed by The Star, Pinoy Exchange, Pioneer Life, Sunbolt, Alaska, Handford and Cebu Holiday Spa, Pohang Badminton Center, Wheels 'N More Badminton Courts and Excel Badminton Center.