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