Umbraco incorrect 'Link to document' when setting hostname

Basically defined a domain (Manage hostnames option) for Node1 and have Umbraco tree structure

Content
     + en
       + Node1
        + Subnode1
        + Subnode2
       + Node2
     + es
       + Node3
        …

When check ‘Subnode1’ properties have that ‘Link to document’ and ‘Alternative Links’ path are inconsistent:

Link to document: /Node1/subnode1.aspx
Alternative Links: http://www.domain.com/subnode1.aspx

I would like to get rid of the folder ‘/Node1/’ in ‘Link to document’, that is returned in NiceUrl and is messing my Url links on pages.

I would like to only have:

Link to document: /subnode1.aspx
Alternative Links: http://www.domain.com/subnode1.aspx

Tried to follow steps in http://our.umbraco.org/forum/using/ui-questions/3505-Change-site-root-node,-NiceUrl-doesnt-change but no luck the only thing I get is:

Page not found
    umbraco tried this to match it using this xpath query'/domainprefixes-are-used开发者_运维技巧-so-i-do-not-work')
    This page can be replaced with a custom 404 page

Hope I get some helpful reply :) Thanks

Try implementing the solution here: http://our.umbraco.org/forum/using/ui-questions/5481-niceurl--3rd-level

Also, did you try to republish the entire site?