Subject line pretty much says it all.
Last night I had five or six designs tagged as Favored. I started a new session this morning, and a few turns along I opened a shipyard to add a colony ship to the queue and saw the list had been emptied.
[Edit 0816 26 March] I made a Support Tool zip without doing another thing in the game after I saw the oddness. Not sure if those are useful in a context like this, or if making them when the game is running makes them useless.