I opted to encrypt my home directory in Linux some time after setting up
Ubuntu on my laptop. My home directory went flawlessly, however, it is
also recommended that you encrypt your swap partition afterwards, and
that did not go so swimmingly. Thankfully,
this
guide
was able to help me out, and I was able to reboot with no further issues.
Hopefully if you are unable to create an encrypted swap partition under
Linux, this will help you too.