Some options are not available on the "File Options" tab in miggui

Most options in the "File Options" tab will be unavailable after the initial data transfer completes for a given project.

A "Sync" can be executed from the main configuration screen of the project to send changed or new data from the source server.

If the options from the "File Options" tab are desired, they can be configured from a new project.
After any project executes, only the following items are configurable from the "File Options" tab:

Disable Login on the Source
Delete Files Not On Source
Delete Trustees Non On Source