🚀 go-pugleaf

Bibliography size in Endnote Plus has a limit of over 32,000
references.  Its indexing system allows very rapid searching,
so combining all your references in one file shouldn't slow
your manipulation of the file too much.  (Although I have only about
850 refs in mine.  After you have read 25,000 papers and entered
the refs into Endnote it may slow down some, I suppose.)

You can use (for example) key words which you choose to index
groups of references.  Then you can in a fraction of a second
create a window showing only that subset of the original library.
If you want to distribute this subset of your refs you can save
it as a separate file.  This ability may eliminate your need to keep
separate libraries.  If so, this will also eliminate your problem
with merging papers to write a paper, and then maintaining separate
libraries for each paper.  I suspect you might find it easier all around
to maintain only one library.

The "formats" to which you refer are the Endnote Styles, which were
written by regular Endnote users using only Endnote.  Creating
new Styles is very easy.  You just edit a Style using standard
text editing techniques with a few added rules, and save the
new file with a different name to get a new Style.

I recommend that if possible you find someone who can demonstrate
Endnote for you using a large library of references.

Tom Ritch
UCLA