If you just want to completely merge the Libraries, preserving the metadata from "both sides" then MrC's script-of-awesomesauce is definitely the way to go.
However...
If the goal is to preserve metadata from "one side" and clone this metadata to "stacks" or "copies" of files from the "other side" (or something like that), then there might be a better way.
Check out the MCFileIngester processor I made for the MCAutoQueue tool.
Basically, it can take a "source file" and clone the metadata over to a "new file" via a variety of handy means. It can use Playlists as the source (and destination) and work through them progressively, so if you have a bunch to do, you could just add them all to a list and let it run on them. So, as an example, if you have FLAC versions in one Library, and MP3 "handheld" versions in another, and you just want to merge the two while preserving the metadata on the FLAC copies, you could just import the ones with the "junk" metadata, and then run this against them to clone the metadata from one copy to the other (or replace one with the other, or other handy options). It can create stacks, and even has a nifty "stack swap" mode that lets you pick which files' metadata to "keep and replace" via MC itself.
Worth checking out. Might come in handy, even after you merge the two Libraries.