Wasn’t the issue with this one that money was changing hands in exchange for a printed, physical book? Like, I know the team wasn’t making money, but it’s understood in fanfic circles that this is a Bad Idea and this was a very high profile (and, sadly, professional-looking) project.
The work is now on AO3 alongside countless other Star Trek fanfics that exist with no trouble. If they’d done that all along, I suspect there would never have been an issue.