Hmm...
There is a LibraryMerge tool in Links, which I think is supposed to merge the 2001 objects into the 2003 library, but I dont know the details of how it works, because I never got the merging process to work on my computer. Im pretty sure it worked for others though, so you could try it. I dont know whether it works on an existing 2003 library that includes custom objects, but you could always try (make backups to be safe!). Pretty sure Lez had a video about the merger, probably worth checking out beforehand.
I always use a different APCD main folder for each different course I work on, but each of them originate from one of two distinctly different types of base APCD folders. 1: a basic APCD with the 2001 objects included, but no custom added objects (this is an APCD that Dan used the librarymerge on, and uploaded at my request, since I couldnt get the library merge to work on my end), and 2: my standard APCD with all my custom objects, but none of the stock 2001 objects.
I struggle to remember the exact details of how I did it when I wanted some of the stock 2001 3D objects on my courses, I only have a somewhat clear memory of how I did it on my first course Amedal, where I wanted some of the basic 2001 3D bridges and perhaps the 3D fences were from the 2001 library too. What I did was to finish my course with my standard custom library APCD in all other aspects, and only then open it with the 2001 APCD, and added the 2001 3D objects as the very last thing before making the final save. Perhaps this could work for you too?
You can find Dan's 2001 object APCD download here:
https://linkscorner.org/phpBB/viewtopic.php?t=348
