I haven't had a problem with them yet. Loadman mentioned a while back that layouts are not backward-compatible, but I think there's still an new malalayout.exe he hasn't released. I remember I got a message once that said "<file so and so> is from a different version, do you want to use it?", and I went ahead with no problems. I actually run both versions (for testing) from the same folder on the same lappy drive.
It's always a good idea to zip up your MaLa folder and store it somewhere, though. Minus ROMs and other retrievable stuff, its a pretty small backup to keep.