I don't have a script, but for your HTML books I suggest adding a .opf file to each one rather can trying to update FBReader's library file directly. This is the XML file that converts a book into the OEB format, which FBReader imports directly into its library for you. It also imports from subdirectories, if you check the search subdirectories option under the general tab of the options icon. By the way, there is now some documentation on how to use FBReader
here. It isn't much more than you can find out yourself by exploring the icons though.
I have looked for a HTML2OEB or HTML2OPF script without success, but there must be one out there.