100% reproduceable. The Warp Drive has on side of the middle reactor 'bubble' where you can actually 'build' something, which I thought was great, since now I can have a nice looking pipe coming out of it. This puts the block you build partially (fully) inside the Warp Drive. I can even separately paint it. Now when I log off and later log back on, the Warp Drive is gone, but the pipe block is still there. When placing a new Warp Drive there, it takes on the colouring of the block that was previously inside the Warp Drive, and makes the WD unpaintable after that. Not putting a block where the game lets me makes things not look as nice, but at least doesn't poof the WD.
Now fixed in A10.5 B2624 https://empyriononline.com/threads/alpha-experimental-10-5-optimizations.69761/