Complete Time Machine restore is only partially recovering my files I recently renamed my home folder on my new MacBook Pro (Retina, 13"). I restarted my computer not realising that it would result in a complete wipe of my drive. Previously having backed it up with Time Machine, I wasn't too worried though.

Looking through the Time Machine backup files, I also did see everything I had had previously saved, and since I have the backup on an external, I restarted the computer and pressed command+R to perform a complete restore.

About 78% through it seemed as if my external drive had failed (not responding, no progress). However, after a few moments my MacBook said the restore had been successful and restarted. Upon logging in, however, I saw that two very important folders were messed up - both of these I had added to the sidebar and the dock. Now, one of them was missing completely (a question mark in its place on the dock) and the other only had one file in it from a day ago. 

Alarmed, I tried restoring the computer again, with the same results. Now even the backup files on my external don't have intact versions of the two folders. Furthermore, none of the data for my apps or any of my settings seem to have carried over.

If there's any way I can recover the two files, I'd love to know.
Launch the Time Machine App, you may see the time line show you backup time, you can navigate the "important folders" at any backup time.

if you find the files you want, just restore it manually.