The most important thing to remember when you are getting started with EndNote is to never save your EndNote Library to a cloud service, such as Google Drive, Dropbox, Onedrive, or iCloud. EndNote Libraries can NOT be saved on the cloud. This WILL corrupt your library. Always save your EndNote Library to your desktop, harddrive or another local drive.
It is not recommended to have more than one EndNote Library. Having multiple libraries can cause problems later down the line, when you may need to Sync your library, use EndNote Online, and can cause problem with version control. It's much better to just have one Library, and use Groups and Group Sets to manage your references.
Backing Up Your Library
EndNote is a complex program that contains a lot of information, and for this reason, it is not infallible. As with any program, EndNote Libraries can become damaged, corrupt, or inaccessible. You should make regular backups of your EndNote Library and save them in a safe location, so that if anything happens to your main Library, you have not lost all your work.
Unlike an active EndNote Library, a compressed backup can be stored on the Cloud. However, you should move these files back to a hard drive on your computer, before attempting to open them and extract the compressed contents within.
To create a compressed (backup) library:
From the File menu, select Compress Library (.enlx).
You will be asked whether you wish to create a backup of your entire library or just a group, and whether you wish to include file attachments or not. If you are creating a full backup, make sure to include file attachments.
Click Next and select the destination where you wish to save your compressed library.
Recovering a Corrupted Library
Sometimes your EndNote library may become damaged or corrupted. This often occurs when your library has been saved on a cloud service or when the data folder has been deleted or moved.
To recover a library:
Close your EndNote Library.
From the File menu, select Library > Recover Library.
Select the library (.enl file) you wish to recover.
Click Open > Save. Give your EndNote Library a new name.
EndNote will display a dialogue box stating the number of records saved. Click OK.
From the File menu, select Open Library.
Be sure to use the copied library in place of the original damaged library.
Click Open - your recovered library should now be ready to use.
Tip: Further in-depth information on library recovery can be found here.