The wiki is described / configured by an object of type
XWiki.XWikiServerClass as you already saw when you edited the
XWiki.XWikiServerXwiki page with the object editor. When you add an alias it actually adds a new object of type
XWiki.XWikiServerXwiki that ‘overwrites’ only some of the properties (e.g. the domain). So the
XWiki.XWikiServerXwiki page can have multiple
XWiki.XWikiServerClass objects, where the first one holds most of the configuration (including the default alias), and the other objects hold the overrides for the other aliases.
Aliases are deleted by domain. When you delete an alias it actually removes the first
XWiki.XWikiServerClass object it finds with the specified domain. This means that if you delete the default alias (or if you try to delete another alias that has the same domain as the default alias) then you loose most of the wiki descriptor configuration (stored on the first object), including most importantly the wiki owner which grants special rights.
You should try to enable the superadmin account from
xwiki.cfg, login with superadmin, check the history of the
XWiki.XWikiServerXwiki page and revert it to the version before the deletion of the default alias. Then, from the object editor, modify the first
XWiki.XWikiServerClass object as you wish and delete the second one (the second alias).