I have a folder on my server that I'd like to copy to another directory. However, after I copy it and navigate to the new folder, some of the directories are RED and I can't navigate into them. I think this has something to do with them creating links instead of actually copying the folders.

cp -a site2.com/httpdocs site1.com/httpdocs

But then some of the sub folders from site2.com/httpdocs are setup as invalid links into site1.com/httpdocs and I cannot navigate to them nor can the webserver display them.

Additionally, I have a permissions error where the copied files have their user set to site2.com but even after CHOWN I cannot get site1.com to display them.