That's the horrible thing about a time war.  It's a perpetual do-over.  The Time-Lords go back in time and plant a new civilization to aid them in the war.  They kick buttocks as a result so the Daleks go back and kill that civilization before they can provide help which brings back all the Daleks that had been killed by the new race.

Then you bring into play Paradox machines and it just gets worse.

Do that over and over, particularly with fixed points, and you rip apart reality allowing the Cthulian horrors of Outwr-Time to breach into this universe.