When I'm working on a multilayer file there is a serious promblem with layers dissapearing. I've never had this issue before version 24.4.2. This is a real problem when working on a big project. Undo and history have no effect.
Could it be that you inadvertently checked the Filter in the Layers Panel? (edit: or rather »Isolate Layers«; I am trying to figure out which keyboard/clicking combination might trigger it without using the contextual menu or the Select-menu, but so far no luck.)