Here's one idea... though it isn't very elegant.
Unfortunately, while MC alllows you to import an MPL, it doesn't allow you to update an MPL. This means that using XSLT to combine two MPLs is needlessly complicated, but here's what you can do:
Export both libraries as an MPL (use the Export Playlist... as MPL). Create an XSLT that combined the two MPLs using whatever logic you prefer. Make sure that you save the resultant "combined" MPL. Now *delete* all the media files from you library. [Yup... delete from the library - not the media files themselves). Then simply import the "combined" MPL and all should be copesthetic.
Yup... i can hear you now: "Delete the media files from the library? What madness!" Hopefully JRiver will add a way to update the library based on an external MPL. Or maybe scott_r will write an "import" plugin to go along with his "MC XML Export".
Or... maybe someone will write you small little plugin that does this one specific task. But I wonder if it's easy to deal with two separate libraries at the same time.
Scott-
P.S. I really wish JRiver opened up the library using something like ODBC. This would make your task a breeze using something like MS Access. I wonder what database "engine" they use? Perhaps their own, making this a lot of work?