I've also been getting this a lot over the last month or so - never before then (pre version 9000). And yes it is because the .xml files are corrupt, and by corrupt what I mean is they become empty, blank files.
I've only been working on 1 game in this period so perhaps it's an issue in the game rather than Stencyl- don't know.
thankfully I have had backups taking me back to previous versions. So whatever happens with the xml file processes needs to be made more robust within Stencyl to prevent this.