Soooo, I´ve found out, what happend !
FYI: If you open up a Gaea project file and delete a few nodes in the graph and then close Gaea by pressing the "X" at the top right window-border - Gaea seems to save the file on exit !
I did just not expect such a behavior, because if you not actively save changes in other apps I use, changes simply will not be saved in the background automatically, when exiting this way. Normally one would get a dialog like "Really quit without saving?" or something like this (pretty much the standard reaction). If you somehow manage to "kill" the app, normally no changes will get saved, either (or maybe only in some recovery file or something)
So maaaaybe Dax can add such an "On exit dialog" for Gaea?