I've been having trouble trying to customize the look of some of my ships, I've found that when I change a ship from the c-store or a non c-store ship by mixing parts from the c-store ship together, I can't purchase it. It prompts me to buy the c-store ship which is already in my inventory and I can't because it says I've already got it in my inventory.

The current example being is that I'm putting the zephyr hull on the Armitage because it makes it look like a giant miranda, and it's not working because of said problem.

Tried this with a few other ships and got the same thing.

I had the same problem on my HEC. I ended up discharging it, then reclaim it, which fixed the problem. If the other ships you're having this problem with are C-Store, try discharging and then reclaiming them. Just make sure you strip all the gear you want off it first.