Ubuntu's installer for a long while set up an "encrypted home directory" using eCryptFS, i.e., file-level encryption on top of ext4. That's the thing Dropbox is finding painful to support.

Migrating away from that to block-level "full disk" encryption basically requires copying all your files. If you're using <50% of your disk and you feel comfortable doing tricks with partition resizing you can do it, otherwise the best approach is to back up your files (hopefully to encrypted media...) and restore them.