In ELinks 0.10.6, the toggle-numbered-links action (listed in the View menu and bound to "." by default) did not mark the document.browse.links.numbering option as modified, so it did not get saved with the default config.saving_style = 3 setting. This has been fixed in ELinks 0.11.0 and later: they mark the option as modified, so if you then tell ELinks to save the options (via the Setup menu or the Option manager), ELinks will save this change too. And I tested that ELinks 0.11.0 loads the new value back as well.
If you instead quit ELinks without telling it to save the options, then it does not save this change either. This is just the usual behaviour of ELinks and I see no reason to make an exception for this option. A config.save_on_quit option might be added but I think that should be a separate enhancement request. The Debian elinks 0.11.1-1 package was the first one after the ELinks 0.11.0 upstream release. According to my tests, the source package includes the fix. So, I think this Debian bug 333339 could be closed as having been fixed in that version.
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