May I suggest to add this method to the org.apache.fop.hyphenation.Hyphenator 
class?
I had to hack FOP and create a custom build for myself, because I need to 
reload the hyphenation files at runtime.
The use case is, that I have a web applications that allows on an admin page, 
to add hyphenation exceptions on-the-fly. In that case the hyphenation pattern 
files are re-created with the new exceptions but need to be reloaded by FOP. 
The below worked for me, please consider adding to the trunk.

Best,
Marc

/**
  * Clear the hyphenation tree cache, in case the underlying data files have 
changed at runtime.
  */
public static synchronized void clearHyphenationTreeCache() {
  hTreeCache = new HyphenationTreeCache();
}

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