Because 'Triquetra' exists in an alternate universe, an alternate timeline there are a few major events that occurred in the original 'Charmed' Show that could never have happend in 'Triquetra.'
1. Everything that happened within the first season of 'Charmed' and the first episode of the second season is 'Triquetra' Canon as well as anything in-universe that predates the first episode of 'Charmed.'
2. Although 'Triquetra' is based off of a timeline established in the Season Two episode of 'Charmed' entitled 'Morality Bites,' only the first part of the episode in which the Sisters initially punish Nathaniel Pratt by flinging dog poo at him is canon as well as the future world of the 2009 Witch Trials. However, the sisters traveling forward in time from 1999 to 2009 never happens and as such they don't learn the lesson of using their powers for protecting the innocent and not for punishing the guilty.
3. Prue never dies. This one should be fairly obvious but the battle between the Sisters and Shax never occurred, or rather didn't exactly happen as such. Whatever the case, the events of season three's two part ending 'All Hell Breaks Loose' never ended with Prue dying. As a result, the Sisters never meet their half-sister Paige Matthews.
4. In the the third season episode of 'Charmed' entitled 'Blinded by the Whitelighter' the Sisters face a warlock named Eames who was hell bent on killing all whitelighters and leaving all good witches unprotected from evil.
Fortunately in the original 'Charmed' universe the Sisters stop him before he can fulfill his plan. Unfortunately in the 'Triquetra' timeline, the girls were too preoccupied with their own lives and problems and Eames was able to carry out his plan, even more successfully though because he and several other warlocks absorbed the powers of a few whitelighters and darklighters and desecrated the heavenly plane to the point of their only being less than fifty or so whitelighters and Elders in the time of 'Triquetra.'
The destruction of most of the Whitelighters and Elders are important because it leads to many problems within Piper and Leo's marriage. Being one of the few remaining whitleighters left, Leo went into overtime having a surplus of extra charges to look after. this leads eventually to Piper resenting him and their marriage dissolving.