SharePoint does not offer FTP access to upload files/folders so this may present a problem. Essentially, the entire project folder that 3D Issue creates, would need to be uploaded to the host server in full for the Flipbook to work as expected.
However, when publishing your Flipbooks to a Microsoft SharePoint environment we would recommend uploading the project folder to a public-facing server and then embedding the web link for the Flipbook on SharePoint through the use of an iFrame.
Embedding them will ensure that your readers must be signed in to SharePoint before being able to view your Flipbooks.