Giving WordPress its own directory – permalinks question and more

Hi there,

I have two projects underway where I’m using the Enfold theme.

I install WordPress in a working folder (called newsite) in the client’s new hosting arrangement. Then when the site is ready to go live, I change the nameservers for the domain name to the new hosting arrangement and then follow the steps in the following section of the WordPress Codex (http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory) entitled ‘Using a pre-existing subdirectory install’ to make the site ‘go live.’

Here’s my question:
The third and last step of the above process is to update the permalinks. Please let me know if I can do this without an issue in both of these projects (links in private content below). Particularly with the second project which has both Portfolio Items and a WooCommerce Shop.

Thank you!