Keep in mind that global layers have a "source" layout. Which is the initial layout you set the layer global in. If you delete the layer from the source layout then it and all the instances on it are 100% gone. But if you delete it from a different layout, not the source, then it will simply be removed rather than deleted.
So if you want to delete it from the source layout then you will have to do some shifting around in order to set a new source layout for that global layer.
A common practice is to create a new layout called "globalUI", or "globalLayers", something to that effect. Which becomes the source for global layers so you don't run into that issue in the future.