I've noticed that the ship designer can be a bit "Fluky"; at times. There have been a few instances now where I'll create a design and add it to my queue only to find it not there later on. It may still be in the queue; but it's no where to be seen and can't be added again.
I think this only happens when I utilize the ship designer from within the Shipyard. Perhaps it's meant to be that way...
In addition, I noticed that I can "Obsolete" core designs; but can only "delete" those I've designed myself.