This is an issue when opening files from a path that goes through symlinks (i.e. symlinked directory). It seems saving and reloading the session "resolves" any symlinked portions of a file path. Before cleanly reloading the session, there's also some weird behavior that makes it sometimes show the same document under the resolved and unresolved path, and there are weird issues with the project view.

This weird behavior surely qualifies as bugs. In addition, I would like kate not to resolve symlinks at all, because I use symlink for organizing messed up directory structures to some degree.