I had a rash of problems with Steam Workshop last week. Could not upload ship designs, disappearing factions, etc. I was going nuts trying to figure it out, including submitting a ticket to support. Suddenly, it all seems to be working again. Go figure...
In looking at old posts on Steam, it seems that the workshop has a tendency to go sideways occasionally and all you can do is wait it out.
Totally different thing and doesn't sound like your problem, but I downloaded some Dune factions that were causing a crash due to the maker not including a ship style for the factions.