Pre-Time War universe
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As noted by historians studying the Daleks, the version of the Doctor's universe that had "first felt the winds of change" preceeding the Last Great Time War was not the same as the universe that eventually survived the conflict. (PROSE: Dalek: The Astounding Untold History of the Greatest Enemies of the Universe)
Discrepencies with the post-Time War universe
One known discrepency between the pre and post-Time War universes was the life of Bliss. In the pre-Time War universe she studied robotics and never encountered the Doctor, (AUDIO: Companion Piece) whereas in the post-Time War universe she studied quantum physics and travelled with the Eighth Doctor. (AUDIO: The Starship of Theseus)
The Tenth Doctor also claimed that before the Time War the universe was full of "pseudo-gods and quasi-deities" which were not present after the conflict. (AUDIO: The Lost)
Access after the Time War
It was possible for time travellers in the post-Time War universe to arrive in the pre-Time War universe. Twice the Tenth Doctor found himself in the pre-Time War universe, firstly when his TARDIS accidentally jumped a time track, (PROSE: Prisoner of the Daleks) and secondly due to being paradoxically abducted by his own future self using George Sheldrake's time tunnels. (AUDIO: Buying Time) The Doctor was able to use a Dalek time machine to fly through the temporal event horizon to return to the post-Time War universe. (AUDIO: The Triumph of Davros'
River Song also once found herself in the pre-Time War universe. (AUDIO: Companion Piece)