The Delete > Delete All Locators tool has been renamed Delete > Delete Locators. It now has an option box that lets you exclude invisible locators as well as locators in reference layers.
When this option is checked on (default), all invisible locators are protected from deletion.
This includes locators on invisible layers, invisible locators on visible layers, as well as locators attached to invisible objects (and therefore invisible).
When this option is checked on (default), locators on reference layers (layer state set to Reference) are protected from deletion.