Hi vijirin,
No problems! When you remaster the folder /etc/skel is the place where all the remastering scripts I know of put your /home/username content, so, when booting from your remasterized cd the /etc/X11/Xsession.d/45xsession script will put back the content of /etc/skel on /home/username.
Cheers.

P.S: The previous content of /etc/skel you erased won´t be recovered, but it doesn´t matter since everytime you do a remaster this content is replaced by your /home/username content.