If you keep going and delete all the pages in the first site it might not work right either. 
Using the folder based multi sites feature you must keep in mind that unlike when you use different host names, once you are logged into either site, IIS thinks you are logged in to all the sites because they all have the same domain and they all have the same authentication ticket issued by IIS and they share the same physical cookie file on the client machine. In .NET code we can detect whether you are logged into 1 site or both sites because we store an extra cookie with the site guid when you authenticate and use a custom identity object to check the extra cookie(s). Also we can name our role cookie based on the site so they don't get mixed up across sites.
When you login to the root site as admin then log into the second site as admin, then for whatever reason you find yourself back at the root site you are still logged in as admin. If you have different user names in each site then logging into 1 site will log you out of the other site.
When using host names you have completely separate physical cookie files for each site so you can be logged into each one at the same time with different user names.
Joe