I have an SSD + HDD combination in my MBP. SSD for OS and Apps and HDD for the User folder. They do backup successfully on an external Time Machine drive. The idea of this backup is among other things to be able to restore your system after a disk failure. That is what happened to my HDD a week ago. But until now I haven't been able to restore the complete system, since I can't get time machine to restore the 2 disks correctly. My first attempt was to boot from the recovery partition and restore the system from time machine. It only transferred the files on the SSD from the backup. Then I tried to copy the files to the HDD from the backup via Carbon Copy loner. That managed to open the user account and see my desktop and files but none was editable, apps like iphoto, mail, Adobe CS5.5 suite didn't even load since they either didn't find necessary files or didn't have permission on others. I did name the new HDD the same us the previous one but nothing happened. To me the only logical way for this to work would be to manage time machine to understand the 2 disc setup and restore accordingly. Is setting up from scratch the only option? Has anybody found a fix to my problem? This question was asked on another thread but I realized it was a very old one so I opened a new one.