It just occurred to me that your labels may be disappearing simply because the editor automatically zooms out to make the arranged diagram fit into the editor area after a layout calculation.
Do your labels reappear if you click the "1:1" button in the tool bar?
yEd does not display labels below certain zoom levels. This is a performance optimization because displaying text is expensive and at very small zoom levels text is not readable anyways so it does not make sense to perform the expensive operation. However, it is possible to turn off this optimization. To do that, open "File" -> "Preferences", go to tab "Display" and set the value for option "Paint Details Threshold" to "0".