Perhaps "deprecated" isn't quite accurate. I could have sworn one of their documentation pages basically said, "there's a good chance you'll run into problems if you use the CLI, and we don't recommend using it." If there was something that explicit I can't find it at the moment. There is [0] that says "please use the in-process runner if possible," [1] discussing problems with the cli migrators, and [2] where the maintainer seems to have a preference for removing the cli's in the long run.
[0]: https://fluentmigrator.github.io/articles/migration-runners....
[1]: https://github.com/fluentmigrator/fluentmigrator/issues/1006
[2]: https://github.com/fluentmigrator/fluentmigrator/issues/1016