Alright, now I see what the situation is. When you relocate the library using Sound Library Manager, Logic would assume that your external drive is now the default location for the library content. In other words, it has already created the necessary symbolic links (regardless of the size of the content initially moved) to the external drive. All you have to do once it's done is keep your external drive connected to your Mac when you download the rest of the library. One note about this process though: the installation packages are downloaded to system drive, BUT installed on external.
So to sum it up, just keep your external drive connected and download the sounds in smaller chunks. Say, 5-10 GB smaller than free space on your system drive (i.e. if you have 20 GB of free space, select 10-15 GB of sounds to download at one time). There is no need to first download and install libraries on the system drive for relocation to external later, in other words.
A recommendation to fix your current situation, where you have parts of sound library both on system HD and external, would be to delete the library folders on external and relocate the library again. After you delete the content on external Logic should allow you to select it as a target drive for relocation. When it's done, continue downloading the library to external as described above.
