Artem2P It can be a problem, especially if you've updated to newer versions of Godot. Always backup your whole project folder first!
An example I've run into when updating to 4.1 and 4.2 is that the GLTF (and FBX and Blender) 3D scene importer will use a few slightly different node names than before, and this can break a bunch of references in your project. And the problem doesn't manifest immediately when you update Godot, only when you delete the .godot cache.