You might have problems with other events that try to give you a default type of ship, such as a colony ship, constructor, freighters, basic warships, basic explorations/survey ships, etc., if the design for them is not available to be used, i.e. you obsoleted it or tried to delete it. So leave them alone. You can make modified copies with different names, but not the SAME name, (i.e. you are trying to overwrite or replace the old design using the Same name, do not try this).
Those events/results/actions (such as draft colonists) expect to find a specific ship name and design (i.e. in a specific game file), and trying to change them in any way (including obsoleting them), can make the event/result/action malfunction, i.e. give NO result.
Leave those default ship designs alone. Any revised/modified copies of them should have different names.