I've encountered this problem myself and there is an easy workaround. Here's what you do:
(1) While Logic Pro is closed, find your existing Library folder that Logic doesn't want to recognize and rename it something else like "Library_backup". Then move it to a different folder than where you want the final library to live. This is important - don't forget this step. You don't want logic to know about your old library files just yet. It has to think you are starting over from scratch.
(2) Now open Logic Pro X. When it gives you the stink about wanting to download the library files all over again - uncheck all of the library parts except for the Reverb Presets. I found that this was the smallest single piece of the library you can install where Logic will leave you the hell alone. It was about a 1gb download. So I downloaded just that and let it install to the default library location.
(3) Now go to the main Logic Pro X menu at the top > Sound Library > Relocate Sound Library. Tell it to move whatever was just installed to wherever you want your final library to live... After it's done installing, make sure to *close* Logic Pro X completely. Otherwise the next couple steps won't work.
(4) Now go back to the location of your library backup and rename "Library_backup" back to just "Library".
(5) Copy/move the large backed up Library to the same location you just moved the newly installed smaller library to - the same location you want the full library to live. When it asks you to replace, simply replace it; overwriting anything that was there before.
Voila - your original sound library is intact in the place you want it where it was before and upon opening Logic, all sounds and instruments are properly detected.
It seems like a lot of steps but I just did this myself and it took only a few minutes.
