There are no "Canon Police" that will take away your D&D licence if you swap campaign elements around.
No, but there is always the complication of new players to the group who don't know what canon you've changed or ignored, even if your group is well versed in it. Sure, you can overcome it, but it ranging from annoying to painful, depending on how much you've tweaked.
I mean, if I ran the Realms, it'd be pretty harsh:
- Five Factiions? Never heard of them. Hate world-spanning organizations. Especially something like the Harpers because good is stupid.
- Lords of Waterdeep? Yeah, as if the rulers of a major city could keep their identities unknown. The city's ruled by a council of guilds. There's some moving in the shadows, but no Illuminati.
- Avatars? Gods walking the world? Stupid. Never happened. Continuity issues? Who cares? Still stupid.
- Drow? Yeah, I guess they exist, but hardly anyone ever sees them. There
definitely have never been any even marginally famous good-aligned drow. No, you can't play one. I'd rather you showed up in a Jar Jar Binks costume and talked in character for four hours.
- Underdark? Doesn't exist. Drow and other critters like that eek out an existence in isolated caverns and have a very hard time interacting with one another.
- Undercity? Pretty hard without an Underdark.
- Elminster? Yeah. He used to talk with Mordenkainen and Dalmar. He was in transit when contact was lost with those worlds. As far as we can tell, he will be feeling the pain of being atomized for the rest of eternity. No, even Ao can't save him.
- Khelban? Yeah, he can stay. I just like the name. He won't be relevant to, well, anything. Ever.
- Wall of Souls? Sure. Might as well have a reason for you to fill in that blank on your character sheet because I know you ain't gonna, otherwise.