I have to admit, that when removing all of roots channels, the handy command-not-found feature will stop to work and throw you an ugly error on an unknown command.
For that to work, roots nixos channel has to stay and kept roughly up to date and that channel has to follow a nixos-* branch that the command-not-found can find its database.
There is an option that would allow you to specify a different location for that DB, though I do not know how to get or build one, as the used DB is different from nix-index.
edit
By accident I found this post again, and I have to add, that I found a solution in the meantime, you can read about this solution in my blog:
https://blog.nobbz.dev/2023-02-27-nixos-flakes-command-not-found/