Ext2 Filesystems Utilities

I have a ~500 GB ext2 filesystem that I wanted to check after a crash. It
had dir_index set and has a quite a lot of directories. While checking I
realized that pass 3A "Optimizing directories" had an ETA of about 5 days.
This was possible by a local modification giving pass 3A progress output.
Then, I killed e2fsck and deleted the dir_index feature with tune2fs.
Checking again, e2fsck reasonably cleared all htree indexes. However,
apart from some other problems, it reported in pass 2:
Duplicate entry '........nf' found.
Marking /sets/2009-06-11T03:05_lar:437/opt/applix/axfonts/sun_snf
(27364312) to be rebuilt.
and in pass 3A:
Entry '........nf' in
/sets/2009-06-11T03:05_lar:437/opt/applix/axfonts/sun_snf (27364312) has a
non-unique filename.
Rename to ........nf~0? yes
Entry '........snf' in
/sets/2009-06-11T03:05_lar:437/opt/applix/axfonts/sun_snf (27364312) has a
non-unique filename.
Rename to ........sn~0? yes

Now here is the e2fsck problem. Doing another check gives
e2fsck 1.41.9 (22-Aug-2009)
Pass 1: Checking inodes, blocks, and sizes
Pass 2: Checking directory structure
Duplicate entry '........snf' found.
Marking
/sets/2009-06-11T03:05_lar:437/opt/applix/axfonts/sun_snf (27364312) to be
rebuilt.

Pass 3: Checking directory connectivity
Pass 3A: Optimizing directories
Pass 4: Checking reference counts
Pass 5: Checking group summary information

backup: ***** FILE SYSTEM WAS MODIFIED *****
backup: 11590540/32152680 files (3.3% non-contiguous),
522271246/522602480 blocks

Running e2fsck again and again gives the same result. The last step is
with a vanilla 1.41.9 without local modifications.

I can keep this filesystem in this state for another few days to track the
problem. Unfortunately I cannot make the filesystem publicly available.
I'm fairly familiar with C programming but have no knowledge of the inner
workings of e2fsprogs nor ext2 layout. What would be the next step?
Please reach me at springl-e2fsprogs@bfw-online.de.

Stephan Springl