as the old fids directories stay big, even if you empty them

To clarify what Pim's saying: As you add files to a directory, the amount of space used by that directory gets larger -- it allocates more space to list those files in.

With the ext2 (and other) filesystem, when you delete files from a directory, the space allocated to the directory is never (or is it just rarely?) reclaimed.

So, if you have a directory that once had lots of files in it, and you want to shrink it, you need to move the contents somewhere safe, and then delete and recreate it, like Pim's saying.