Right, a replay file contains the level. If you open the replay file as a level, e.g., by moving it into the level tree and selecting it in the level browser, it will be that level. When Lix interprets a file as a level, Lix will ignore the replay lines in the file.
On one hand, it's handy to always have the exact version of a level right in the replay as a backup.
On the other hand, it's confusing what exactly a file really is.
The mass replay verifier will even ignore the included level and always run the replay against a file in the level tree. These special rules (when will Lix use the included level, when will Lix use the pointed-to level?) make the system hard to understand. In the replay browser, there are two buttons to work around this ambiguity: "Play" to replay against the included level, "Pointed-to level" to ignore the included level and replay against the level in your tree.
-- Simon