Genesis timeline

Some accounts suggested that the Fourth Doctor's mission to interfere with the creation of the Daleks on behalf of the Time Lords created an alternate timeline, leaving behind the original version of history altogether rather than merely altering it. This was never reversed. (PROSE: A Sourcebook for Field Agents) By another account,according to the Celestial Intervention Agency's own documentation, the mission to Skaro had ended up a bootstrap paradox, as the Doctor's actions only ensured the timeline they were already living in had come to pass. (PROSE: The Dalek Problem)

The Time Lords observed that changes to the timeline had freed thousands of worlds from the tyranny of the Daleks, but not the millions hoped for. Following the Doctor's subsequent actions in the weapons research facility of Deepcity, however, the Time Lords foresaw the rise of a race of robots that would challenge the Daleks and lead to the fall of the Dalek Empire. (PROSE: A Device of Death)

Regardless, numerous observers including the Doctor themself saw the mission as the "first shot" (AUDIO: The Dalek Conquests, The Innocent, The Eternity Cage, PROSE: Engines of War, The Astounding Untold History of the Greatest Enemies of the Universe, COMIC: Hunters of the Burning Stone) of what ultimately became the Last Great Time War, a conflict which had far-reaching consequences across the history of the universe. (PROSE: The Whoniverse, The Astounding Untold History of the Greatest Enemies of the Universe, Dalek Combat Training Manual) Indeed, the Daleks did at some point become aware of the Time Lords' attempt to subvert their development, which they henceforth viewed as the Gallifreyans having launched a pre-emptive strike and act of aggression. (PROSE: The Slyther of Shoreditch, WC: , AUDIO: The Dalek Conquests, The Innocent, The Eternity Cage) The Tenth Doctor later admitted that, for the Daleks, their history was "confusing enough" before the Time War. (PROSE: Prisoner of the Daleks) In a parallel universe in which he chose to destroy the Daleks, the Fourth Doctor was embroiled in the Time War as it started prematurely, regenerating into the Warrior. (AUDIO: Dust Devil)

By the Time War, there were some Gallifreyan scholars who believed that, had the Time Lords allowed the Dalek timeline to evolve without interference, and so let Davros refine his creations at that early crucial stage, then they might have become the less aggressive creatures that had sought to create. (PROSE: Dalek Combat Training Manual)

Behind the scenes

 * The Discontinuity Guide made the claim that, originally, Davros was killed and forgotten, and that the Fourth Doctor's interference with the creation of the Daleks created a new timeline where Davros survived, the Doctor's warnings about the Daleks having made Davros paranoid enough to activate a force field in his chair. As a result, whilst the Daleks originally had a solid, cohesive empire, always with one purpose, Davros' presence reduced them to "a mess of squabbling factions" which were "incapable of the unity needed to develop dimensionally transcendental time travel." Published before the Last Great Time War was established in Doctor Who lore, The Discontinuity Guide went on to claim that "whilst Davros lives the Daleks will remain disorganised, and will never become the threat that the Time Lords so feared."
 * The Dalek Handbook speculates on how the Doctor's interference, dubbed the "(re-)creation of the Daleks", changed the timeline, whether the Daleks were indeed set back a thousand years or if history played out more or less the same. As the Doctor did not hear Davros mentioned prior to the Genesis Incident, it was likely that Davros was exterminated and forgotten in the original timeline. As the ruins of the Kaled City still stood during the Movellan Incident of the early 46th century, it was suggested that the city of Kaalann had not yet been built in this timeline while noting the absence of Thals and continued presence of radiation, indicating the neutronic war was even more devastating in the new timeline. The apparent absence of the Dalek Emperor during the Imperial-Renegade Dalek Civil War is taken as evidence that the Daleks may or have not avoided the Dalek Civil War in the new timeline.
 * In a deleted scene from the end of Return of the Cybermen, the Time Lord messenger would have appeared in the TARDIS to tell the Fourth Doctor that his failure to succeed in his mission had caused his own history to reoccur in slightly different ways and may lead to a Time War. This was meant to explain the contradictions between Return of the Cybermen and Revenge of the Cybermen, as well as between The Haunting of Villa Diodati and Mary's Story, and Human Nature and Human Nature.