Gonna have this in a spoiler box so this post won't be that big/long unless someone opens this.
The Hatamoto Family Luxury Liner Serial Murders (Volume 3, File 20–File 25)
The Kidnapping of Conan Edogawa (Volume 5, File 49–File 50 and Volume 6, File 51)
The Night Baron Murder (Volume 8, File 72–File 77)
The Great Detective of the West Appears (Volume 10, File 92–File 96)
Encounter with the Black Organization (Volume 12, File 114–File 116)
Murder at the Ski Lodge (Volume 14, File 139–File 140 and Volume 15, File 141–File 143)
Conan Vs. Kaitou Kid (Volume 16, File 156–File 159)
A New Student (Volume 18, File 176–File 178)
Shinichi Kudo's First Case (Volume 21, File 204–File 207)
The Cruise Ship Symphony Serial Murder Case (Volume 23, File 225–File 230)
The Desperate Revival (Volume 26, File 254–File 257)
The Mysterious Passenger (Volume 29, File 287–File 289)
The Tiger Scroll and Toyotomi's Castle (Volume 31, File 317 and Volume 32, File 318–File 321)
Deja Vu in the Rain (Volume 34, File 347–File 349)
The Dark Footprints of a Silent Witness (Volume 37, File 377–File 379)
Ginko-Colored First Love (Volume 40, File 410–File 412)
Dual Mysteries on a Full-Moon Night (Volume 42, File 429–File 434)
Miracle at Koshien Ball Park (Volume 43, File 445–File 446 and Volume 44, File 447–File 449)
The Dissonance of the Stradivarius (Volume 46, File 470–File 474)
Black Impact (Volume 48, File 499–File 500 and Volume 49, File 501–File 504)
Deduction Battle on the Ski Slope (Volume 50, File 518–File 521 and Volume 51, File 522)
The Young Witness and the Giant Hammer (Volume 53, File 550–File 552)
Whereabouts of the Missing Photograph (Volume 56, File 582–File 584)
The Magic Spell of Friday the 13th (Volume 58, File 605–File 608 and Volume 59, File 609)
Kaitou Kid and the Purple Nail (Volume 61, File 631–File 634)
What She Truly Wants to Ask (Volume 62, File 652 and Volume 63, File 653–File 654)
Detective Boys Vs Robbers (Volume 65, File 677–File 679)
Tomorrow is There (Volume 67, File 699)
Ryoma's Treasure (Volume 70, File 731–File 733)
Holmes' Revelation (Volume 71, File 743–File 751 and Volume 72, File 752)
The Besieged Detective Agency (Volume 73, File 771–File 773 and Volume 74, File 774)
Detectives’ Nocturne (Volume 76, File 796–File 800)
The Shadow Approaching Haibara's Secret (Volume 77, File 815–File 817)
The Cherry Blossom Viewing Trap (Volume 80, File 850 and Volume 81, File 851–File 852)
The Tragedy of the Red Woman (Volume 82, File 872 and Volume 83, File 873–File 875)
Scarlet Prologue (Volume 84, File 891–File 893)
The Woodpecker Murders of Kawanakajima (Volume 86, File 913–File 915 and Volume 87, File 916–File 917)
Shukichi’s Envelope (Volume 89, File 945–File 947)
Ripples (Volume 92, File 972–File 974)
And this is just one way to do it—and you may also want to look at the cases that immediately precede and immediately follow the ones listed—for instance, the case where Hyoe takes notice of Rumi due to her public take-down of Mr. Golfer culprit ended 25 files before the end of this case... and File 1,012–File 1,014 is 25 files after Rumi and Hyoe's encounter back in February.