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Hi there,
I'd recommend that you save your library by using the Compress & Save feature. What version of EndNote do you have? If you have a newer version of EndNote, you can find this option under the File menu. It will be called "Compressed Library" or "Compress and save." This will create a file with the extension of .enlx
You can email your advisor this library (or he/she can email you their compressed library).
Then whoever receives the other person's library will want to follow these steps after having both libraries open:
Once you have merged the two separate libraries, be sure to re-name it something distinctive and then compress and save it before you mail it back to the other person. When sharing libraries, I often use today's date in the title of the library, so I'm always sure to use the most recent version.
Note: EndNote recommends only merging libraries when both users are using the same version of EndNote, ie. EndNote X6.
Hope this helps, and let us know if you have any questions.