Like Sebastien mentioned, the library file is SQLite. I dug around in my own catalog and found that AgLibraryKeyword table. There are three columns you care about: id_local, name, and parent. As you might expect, parent points to the id_local of the parent keyword. In my library the "root" keyword has id_local 73.

So, assuming you had something like this:

  id_local | name    | parent
-----------+---------+--------
  12345    | animals | 73
  12346    | birds   | 73
  12347    | eagles  | 73
  12348    | parrots | 73
  12349    | falcons | 73

You could "fix" the hierarchy like so:

UPDATE AgLibraryKeyword
    SET parent = (SELECT id_local FROM AgLibraryKeyword WHERE name = 'animals')
    WHERE name = 'birds';

UPDATE AgLibraryKeyword
    SET parent = (SELECT id_local FROM AgLibraryKeyword WHERE name = 'birds')
    WHERE name IN ( 'eagles', 'parrots', 'falcons' );

This would end up as Animals > Birds > Eagles, Animals > Birds > Parrots, and so on. The table ends up looking like this:

  id_local | name    | parent
-----------+---------+--------
  12345    | animals | 73
  12346    | birds   | 12345
  12347    | eagles  | 12346
  12348    | parrots | 12346
  12349    | falcons | 12346

It's not as manual as doing it by hand through the UI, but it's still going to take some work. Should be just as functional though.

I should note that while investigating this, I made similar changes a few times that didn't seem to take. I'd suggest saving your SQL to a file so you can re-run it if it doesn't seem to work the first time. And, of course, you should back up your library ahead of time :)