What you can do is mark it obsolete after you start to retool the shipyard. (You can't retool to an obsolete design.) The civies won't build obsolete designs but you can.
my problems started when I put a cargo hold on a tanker-- the civvies started purchasing tankers en masse. I've got 17 of the buggers before I realized what they were doing. They split items up frequently enough that I've linked that to most of my problems.
I'm having an annoyance of labs. I move labs to research worlds. Sometimes I have the civvies do the moving, sometimes I move them. I've noticed rounding issues. Somehow I ended up with .9 labs at a destination, so I get an unallocated lab warning every turn. I can't build 0.1 labs, it seems to vanish on completion. I moved in some extra labs, and now i'm left with 0.01 unallocated labs on one world and 0.89 on another. I would really like to get rid of the partial, but I cant figure out how to do so in SM mode-- the button to instant production is grey'd out and I haven't found any other relevant details...