From En X3 help:
Merging Libraries
There are three ways to merge libraries: import one library into another, copy references from one library to another, or drag-and-drop.
Any time you add references to a library, the newly added references are assigned new record numbers in the order that they are added to the library. This means that a reference that was #23 in a smaller library, could become #600 in a larger library. As a result, you cannot use the larger, merged library to format papers that have citations with the older record numbers.
Note: Before merging libraries, it is a good idea to make a backup copy of the library into which you are transferring references.
Tor previous versions, see your EndNote help manual.