The other two things I thought of that happen semi-regularly:
Press / and make sure you’re not editing in “local” mode. This allows you to see one object instead of your whole scene. It’s really handy when you’re modifying interior details of something, and there’s a frame in the way. (Like the motorcycle I’m working on.). But if you’ve forgotten you’ve done it it can be disconcerting trying to find everything else.
Also press Alt-H and make sure you haven’t accidentally hidden anything. Do that both in object mode and in edit mode as you can hide whole objects in object mode, and individual vertexes in edit mode.
Other than those tips we may need to see screen shots of what’s happening in your scene.
