Hello!
I’ve been working on a ship since some days. Yesterday I started to make the windows. These windows are made by cylinder but after a while I can’t make normal holes with negate.
Sorry for bad english,
Thanks for the comments in the future! 
Unions are highly inefficient compared to bricks for this sort of thing. Too many negations and your part will look screwed up and not function as well either in terms of being able to walk through it, etc. I suggest separating the part into several unions and then translating those into meshes.
As @hugh_capet said, unions are not made for many operations.
I would suggest exporting your model and editing it in blender or other 3D modelling program.
You will have better control of the mesh, and it’s not likely to randomly disappear.
Yes I’ve cut the union in two parts, thanks guys, it helped
