Do not do this manually!
Let fsck take care of things.
Best scenario: You have BackupMenu installed and you have a Debian- or Ubuntu-PC or -Live-CD at hand: Start your N900 with the keyboard out, type 'w' to export the internal microSD to your PC read/write. Then run fsck from the PC on your second partition of the N900.
You could also try to fsck from BackupMenu, but i had no success with that (but did not try it recently).