Hi Itai,
A recovery from a backup of the RDF files, or rebuilding the project
from source is the only reliable way to fix these corruption problems.
Usually you'll find that one or more files have been completely
truncated due to a write failure to the full disk. So far as I know
we've never found the root cause of the corruption, but I suspect it
deep in the Jena code.
Please take a look at the recent documentation I added on the various
backup options:
http://wiki.controltier.org/wiki/
Backing_up_ControlTier ... in particular, we find the ZipBuilder based
RDF database backup method very useful.
Anthony.