I re-added the catalog when doing a 'Refresh All Catalogs' - the designer thought it was new even though it was already added to the project so I ended up with two references to the same catalog. It couldn't find the old one and suggested I rename it.
- Did you rename the catalog at LLBLGen Designer's Catalog explorer?
Well that fixed the problem. I removed the new copy of the catalog, added '2' to the name of the usual one, did a 'Refresh All Catalogs', cancelled out of it and then re-named the usual catalog back to its correct name, did another 'Refresh All Catalogs' and all seems to be back to normal.
So possibly the project had a corrupted catalog name.