I have "successfully" moved my encrypted home to a separate partition using the instructions here: How can i move an encrypted home directory to another partition?

However, some files are not being copied over. Most notably, I have a directory in my old home that contains the themes I use. This directory and it's contents are not copied over to the new home and therefore I come up with the default theme. Permissions on the directory that was not moved are identical to the other directories in home. Another discrepancy is that my Dropbox folder came over empty and had to resync itself. My concern is what else might be missing from the copied home. At this point, I've flipped back to the old home by re-editing /etc/fstab, but I'd really like to get /home cleanly and completely off of root without having to core the system.