This game taking place directly after
Crash Bandicoot: Warped (1998) does not completely retcon the events of
Crash Bandicoot: The Wrath of Cortex (2001), as that game served as an indirect sequel. Furthermore, although the 100% completion epilogue does reveal some plot holes that contradict the events of the original timeline following
Crash Bandicoot: Warped (1998) (for example, Dr. N. Brio getting stuck on display in a museum in his pterodactyl form without an explanation as to how he becomes human again by the time
Crash Twinsanity (2004) takes place),
Paul Yan has confirmed that the games that made up the original timeline following
Crash Bandicoot: Warped (1998) are still canon.