I hear you.
I'm having to completely redo my original ship set to fix it. You may already know how to avoid the issue in future, but just in case, for anyone reading.
To avoid many possible issues when designing large numbers of ships.
1) Always build off of one ship component. Do not attach multiple components to your original cube. (necessary for any big animations you might want later)
2) Start a game, press "`" type "unlock". This gives you all techs, then proceed to design your ships and save them as templates. If you need to stop and come back... start a whole new game and repeat. You cannot trust a save game, you will often find parts you start to add have a new/blank color.
3) Recommend a naming convention for grouped parts, slightly different than your ship designs. For example "TS-C-Bridge" is a TS component. Whereas "TS-Small 01A" is the first small template ship for the same race. This will help group things easily in your design folder.
4) Before saving a ship or component as a template, always build a copy. Clipping errors, and visual artifacts because parts are too close together, will not show in the editor typically.
5) Good floating dimensions for ships is a Y up/down Oscillate of 4.0 with speed 1.0 or -1.0
6) Currently in order to delete a template, I'm having to open the designs folder and remove the offending template, WHILST THE GAME IS RUNNING. This is new since Beta 5 and quite inconvenient. Crashing after exiting a game after doing this is common... but otherwise I find the templates reappear if I only delete them when the game is not running.
If your the type of person that wants to design ships as they play, I feel for you, your going to run into the coloring bug. Best to just learn to sit down and build out an entire ship set. Just my 2 Cents.