Not sure if this bug still exists.
I’ve had this bug happen quite a few times, thought I might have made a mistake on my own, but then I caught it red-handed about 2 months ago. But I have no idea how it happens.
Simply work on multiple level files over a period of time, and then import some .t3d files during a work session. If the level has already saved directly after importing a t3d file, then you can look at the top-left and the level name itself might have changed (it overwrites other map files in the folder, I think.)
Other than with importing .t3d files, I don’t remember the level name itself changing.
As a sanity check, I personally would go in the editor code and add a save lock/forced crash for a time after importing files, and then see what happens over time. But I didn’t get round to looking at the codebase with other things to do.
I have just avoided using multiple levels at all since this, so I thought I would report it.