So unfortunately I don’t have much info to back this one up, but the game somehow deleted a ship I designed. I had used a Dreadnaught hull in a prior scenario (thus already saved) and went back to update it in the ship editor.
I swapped some modules, saved it, then went to go into battle. No design with that hull was available, and it was like I had never worked on it in the first place.
I suppose there always is the chance I’m an idiot and somehow accidentally deleted it, but I don’t believe so. Figured I’d make a post in case anyone else experiences it.
I have seen this as well. It usually happens if you switch between the Module Placement / Visual / Main Menu to many times.
The only way to get the ships back is to restart the game
Thanks for reporting this., If anyone nails a reproducible set up steps that triggers it, and I haven’t already posted here to announce a fix, pls let me know 
Well, the ship reappeared, and Darkstar was correct in that I was tabbing between the visuals and modules a couple times.
Just thought I’d add to this by mentioning that, if you select a battle and the game tries to load the most recently used deployment, but the deployment includes a design the game has briefly lost, it will crash. So the game never completely forgets a design, however briefly.