In Batman vs. Robin, Dollmaker has the appearance and M.O. of Dollmaker III/Barton Mathis, a Batman villain in the comics, but the name of Dollmaker II/Anton Schott, who was a Supergirl villain, along with Schott's M.O. of turning children into killer dolls. His backstory continues this, with his father being named Toyman/Winslow Schott, but being a serial killer closer to the comic book's Wesley Mathis.
According toWord of God, the Kid Flash who appears in the prologue of The Judas Contract is a teenage Barry Allen. This means that Barry takes Wally West's place as the original Kid Flash who helped found the Titans, as well as his resultant friendships with Dick Grayson, Beast Boy, Roy Harper and Bumblebee.
Also since Bumblebee and Beast Boy were shown in the prologue, they seem to replace Donna Troy (who appears in a non-speaking cameo at the end of the film) and Aqualad (who only appears in the Flashpoint timeline).
Superboy seems to feature the wardrobe and personality of the Post-Crisis Conner Kent, but his overall design is closer to that of the DC Rebirth Jonathan Kent, albeit a teenaged version. As well, he's working with Luthor, similar to how the Matrix Supergirl did during that time.
Both Bertron's role in Superman/Doomsday: Hunter/Prey as Doomsday's creator and Mongul's role as the power backing Cyborg-Superman are given to Darkseid.
While Barbara Gordon was in the comic, there she was Oracle. In the film, she's Batgirl and takes Huntress's role with Alfred and Dick subbing for Barbara's comic role. Likewise, Damian Wayne replaces Tim Drake.
While Lady Shiva and Lex Luthor did appear in the comic, here because of Ra's al Ghul's death at the start of Son of Batman and Talia's death in the climax of Batman: Bad Blood, Lady Shiva replaces Ra's as the one informing Batman of an outsider's use of a Lazarus Pit and because he joined the Justice League at the end of Reign of the Supermen, Luthor replaces Talia as Batman's Lexcorp contact (in the comic, Luthor was President Evil at the time).
The Riddler replaces Tommy Elliot as Hush, originally a scrapped idea from the original comic.