Every time you make a backup copy of a library - it keeps the same file name and adds copy - so you could end up with ......copy.copy. When you save a copy either rename your EN library with a unique name or add the date after copy so you know when you made a copy.
When working with EN files it is the same process as working with other files - EN will overwrite files with the same name or create a new file when the name of the file is unique.
Synchronizing (Sync) your EN library to EN Online is another option. This will allow you to automatically backup any changes you make to your EN library and also sychronize to another computer.
See EndNote Online in this guide.
Your EndNote library is saved when you create it. This is made up of 2 files. One is the library name.enl file, the other is the library name.data folder. You will open and work with the .enl file but the .data folder will contain any pdfs stored in your library, the trash file, groups, term lists, etc. It is important and must not be removed or renamed unless you are deleting your library.
There are 2 options to make a backup copy of your EN library: