You would end up with the desired results based on the steps you mentioned.
If you needed the 600 references again later, you could restore the backup and manually move over any you wanted to have in your library or even import the backup into the current library and discard duplicates to net the missing references.
You can find information on merging libraries in our Knowledge Base online:
“(Optional) If you want to import only a subset of references from a library, first open that library and show only the references you wish to copy. For example, if the library says, “Showing 10 out of 200 references,” EndNote imports only 10 references. If the library you are importing is locked or in “Read-Only” mode, all references are imported regardless of what is currently showing.” and then
“Open the library into which you want to import the references”
So we can have multiple libraries open at the same time?
You can have more than one library open at a time and use the Window menu to allow you to switch between them or on Windows force them to show up side by side or one on top of the other.
To be honest, I wouldn’t try to maintain a library removing records you use less often. Then you need to find them again when you unexpectedly need them. It is far better to keep one library with all records you have used. Furthermore, if you need to revise or rework something later, you will be frustrated if the current library no longer contains all the records you cited. I have been using the same library for the over 25, probably 30 years (yes, that isn’t a typo) years, from the days when Endnote was DOS program!
It is my understanding, there is an unlimited number of references in our library and an unlimited amount of storage for file attachments and figures. (since X7)
from my Endnote helpfile:
Important Points to Know About the Sync Process Sync includes an unlimited number of references in your library and an unlimited amount of storage for file attachments and figures.