I do not understand fully.
If there is a part update you can download the modified new files (http://www.ldraw.org/parts/latest-parts.html) or the complete library.
Oh, now I understand
you do not know which parts of the update are new and which are updates.
I am sure there are applications that can compare the content of two folders. Then you have to copy the modified files to your library and the remaining files needs indeed work by hand as the sort order you use (which I like) is only possible in this way.
If there is a part update you can download the modified new files (http://www.ldraw.org/parts/latest-parts.html) or the complete library.
Oh, now I understand
you do not know which parts of the update are new and which are updates.I am sure there are applications that can compare the content of two folders. Then you have to copy the modified files to your library and the remaining files needs indeed work by hand as the sort order you use (which I like) is only possible in this way.