SD-card messed up?
Files suddenly in a sub-folder?
Recovery cannot find backups or ROMS anymore?
That is a problem I run into myself after the first trials with my new ROM. What I found is that flashing the latest CWM or TWRP recovery solved the problem without copying around all the files on the internal SDcard.
Try to get the latest CWM or TWRP recovery and flash it.
TWRP V2.4 can be found in A1 kernel
A link to the latest CWM recovery can be found in the CM10.1 nightly
thread. Look for CWM: