ELinks instances connect together so that they share the cache, bookmarks, cookies, configuration, etc. Only the "master" ELinks instance does any real work and any other ELinkses you run will only connect to this instance. So when you want to restart ELinks, make sure you have no other ELinks instances running.

Alternatively, you can use the -no-connect parameter to make ELinks always run standalone, or create a parallel group of ELinks instances with the -session-ring N parameter (where N is a number larger than zero). Be aware of that in those cases ELinks won't touch any configuration, bookmark, cookies, etc. files. You can force that with the -touch-files parameter, but beware that this can result in data loss! (For example, when two master ELinks instances try to save the bookmarks, and you add a bookmark to each of those, only one of the bookmarks survives.)