You might want transfer your references between Zotero and EndNote if:
Please note that PDFs do not export between programs - only citation information.
Zotero to EndNote
EndNote to Zotero
It is important to fully understand how Zotero stores its data so you can correctly back up your Zotero library. By default, your entire Zotero library is stored in the 'zotero' directory of your Firefox profile. The most important file in this directory is the zotero.sqlite file, which contains the majority of your data: item metadata, notes, tags, etc. The directory also contains a 'storage' subdirectory, containing all of your file attachments, such as PDFs, web snapshots, audio files, or any other files you have imported (note that files that are linked are not copied into this subdirectory).
Your 'zotero' directory will likely contain several other files. These can include zotero.sqlite.bak (an automatic backup of zotero.sqlite, which is updated when you quit Firefox and the existing zotero.sqlite.bak file hasn't been updated in the last 12 hours) and zotero.sqlite.[number].bak files (automatic backups of zotero.sqlite that are created during certain updates to the Zotero extension).
Warning: Before you copy, delete or move any of these files, be sure that Firefox is closed. Failure to close Firefox before moving these files can damage your data.
Syncing your library means backing up your citations on Zotero's server. This way you can access your citation remotely and retrieve them if something happens to your personal computer.
In Zotero for Firefox and Zotero Standalone, you will see a green arrow on the right side of your application. If you click on it, it will spin to indicate that it is uploading your citations.
Follow the instructions below to sync your library.
If you're regularly using more than one computer in your research, Zotero's sync feature can keep your library up to date on all of them. Zotero can store a copy of your library on the Zotero.org server and check it for updates whenever you open your library on a different computer. All your computers must be running the same version Zotero and be configured to sync to the server.
For more details and help troubleshooting sync problems, check the Zotero site.