Yes! The wonderful Flip PDF Plus Pro allows users to host their publications on their own server.
You can upload all the book files to your own server via a third-party FTP tool, like FileZilla.
On the left panel of FileZilla, you can access your files on your computer.
On the right panel of FileZilla, you have the files and directories from your server.
To upload your flipbooks, you can simply drag and drop the entire book folder to a specific directory on your server.
When the uploading is finished, you can view your flipbooks on your own website and host your own publications on your own server.