I forgot to mention a few more points. 1) fsck -y isn't designed, at least in single pass mode, to ensure the filesystem is completely fixed (see next point), It is designed to make sure that further writes to the fs don't make it worse, among other things.
2) After running fsck, and it reports, "FILE SYSTEM MODIFIED", you must run fsck again to make sure you don't have further errors. When running fsck it must be run, repeatedly until you no longer get the message above. Only then are all the problems with the fs fixed.
3) If you have in the list of messages a note about hard link count being wrong and the count is too few, you *will* cause the deletion of the file, by using the -y fix. This, on a file that would have been totally recoverable had you not chosen the -y option.
4) In the particular case at hand, where there are multiply linked files, you may also wind up rewriting over the top of a good file with information that is not good, hence causing you to lose a file, had you chosen to not clone the file. The opposite is also true.
Lastly, my source for my notes comes from the linux-ext4 mailing list, but what do those guys know anyway?
Jack