This feature has a fairly nasty bug.
If you delete something in build mode, the game will think it's been destroyed, not deleted. therefore it'll tell you the ship is severely damaged, and those deleted blocks in the repair window will be present as damaged blocks. If you repair, these come back.
So it seems whenever doing changes currently, you need to repair, then do changes, then go to the repair window and hit discard.
Otherwise though a lot of stuff here that needed to be done. Keep up the good work!