The master development branch of Ardour has recently been merged with two major development branches. These bring major new functionality to Ardour (tempo ramps and VCA masters, among other things), but the result is a new version of Ardour. This version is sufficiently different that it could alter/damage your Ardour configuration files and may not correctly work with existing sessions. We have therefore tagged it “5.0-pre0” so that it will create new configuration folders and not interact with your settings and preferences for older versions of Ardour.
For the time being, the nightly builds should be considered for use ONLY on throw-away material, and should NOT be used to work on existing sessions unless they have been backed up and you are interested in helping us debug issues with the new features (which of course is most welcome).