I am not quite following the problems you are having.
In the Library Manager, there is a button that allows you to "Export selected library items into local folder".
So you can save your 'Embedded' files into your local system library folder and then this folder is simply loaded into any other file you are working with - as one single library.
No it is not an LCF but does that really matter?
As you have discovered to edit an LCF you have to extract it, add or amend the files and then re-create it (there are commands in the menus or the GDL toolbar has buttons for this as well - no there is no extract or create LCF in the library manager).
The only advantage of an LCF is that it is one file and possibly it may load a little faster - but I don't think you will notice this with today's machines unless it is an exceptionally large library.
Loading an LCF or a folder containing separate objects makes not difference once it is loaded, and the loading process is exactly the same.
My 'custom company' library is just a bunch of GDL objects in folders - not saved as an LCF.
This is stored on a server that everyone can access and the library can be loaded into any job.
In fact I actually have all user machines synchronise this library to the local hard drive and load it from there.
Loading from the local hard drive is faster and the synchronising of the folders (library) can be automated with software.
By not having a single LCF file, the synchronising software can copy just the amended or new files rather than the whole LCF file every time there is a change.
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