I installed rEFInd on my new Macbook Air which I planned on using to do a duel boot to linux, but prior to installing linux, I decided to encrypt my drive. I knew I was going to do this, so I had already installed rEFInd with the --esp option. When I rebooted after this however, I t seemed to have deselected rEFInd for boot. I reinstalled, but when I did and rebooted, my Mac partition would not show up in the bootloader (only the recovery partition). I ended up needing to hold Command+Options+P+R to get it to boot again. Any help getting these two to work together would be much appreciated.
Have you re-installed rEFIt after turning on the encryption?
I would suggest getting both OSes working with rEFIt and then turning on the disk encryption.