Instead of being stored in the channel record itself, a channel encoding is stored separately under the [Encodings] group. This is should be in the channel record. Additionally, the format is ugly, eg: "ServerGroup 1 #konversation=UTF-8". This will only continue working as long as the ServerGroup id doesn't change.
The design of this and the practical reasons for it were discussed at length last year in #konversation. The note about the id is also incorrect - the only requirement is that the contents of the file are self-consistent, because it's read in at app startup to build up internal data structures, and flushed out to disk again in a self-consistent state later.