My installed premade ships are preventing an update of KSP with RO from 1.2.2 to 1.3.1. What should I do?

[Grant Exploit]

Hello,

Yesterday, I found out that about a week and a half prior, Realism Overhaul had (finally! ) been updated for 1.3.1. So, I did this sequence of events (I'm on Windows 10, BTW): 

1. Backed up saves and screenshots for safety,
2. Deleted my copy of CKAN and the CKAN folder, as it was malfunctioning.
3. Recalling the tumultuous experience I had with upgrading to 1.2.2, I uninstalled KSP and reinstalled it as 1.3.1.
4. I reinstalled CKAN.
5. CKAN recognized the mods that still existed in the Game Data folder, but (presumably because I deleted my CKAN folder), they were marked by 2 capital letters (which I can't recall) and I could not do anything with them.
6. I permanently deleted all the Game Data, as I always have very little space on my computer. This took with it all of my custom engine configs, yaay... 
7. Now I could reinstall the mods. I attempted to do so, but it kept aborting the procedure as the mods were attempting to install a craft that was already in the Ships folder, which also strangely wasn't swept away by the reinstall.
8. I sent the craft to the Recycle Bin.
9. I tried again. This time a different craft showed up.

What should I do? Should I delete my Ships folder or just the contents? What about the stock crafts or pre-made crafts that may not be provided in 1.3.1 RO?