I agree with Brian, except in very narrow circumstances there's no reason to have multiple libraries, it just creates issues like the one you're seeing. Multiple libraries are inconvenient in a lot of ways: you will hit other roadblocks with remote control, the JRiver android apps, and client/server usage.
MC's database system and view creation system are very sophisticated, you can slice a single library lots of different ways based on almost any criteria you can think of. If you could explain why you want two libraries (what problem are you trying to solve with two libraries?), we will likely be able to help you do what you need with one library, which will be easier in the long run (and will obviate your original problem). Which is to say that you probably have an
x/y problem; Y can't be solved (to my knowledge), but we might be able to help you with X
NB: The main valid technical reason to have two libraries is if you use a client/server setup but need to import/process files and/or rip CDs on a client machine. Then you absolutely need to have a local library to handle ripping/imports because of technical limitations of the client/server model. But except for that and a few other corner cases, there's really nothing you can do with two libraries that you can't do just as well (or better) with one.