I decided to do something similar, today (6, Feb). Uncanny, right? I renamed my X-plane 12 folder and downloaded a 2nd copy to the original location: E:\X-Plane 12. My initial goal was to rebuild the sim over time, as I've done in XP11, once. However, I wanted to make sure I had all my preferences and profiles available so that I could drag stuff over to save time. That didn't work.
I should mention that I was compelled to perform these steps. My last flight ended in a CTD 3/4 into a 2-hour flight. Arggh! I'd had enough and was tired of these seemingly random CTDs in 12.9.x. After spending a bunch of time working I get the feeling that I wasted my time. In my haste, I wound up dragging my Aircraft folder, Custom Scerney folder, and Plugin folder, as well as parts of my Preferences folder back to the new install. Thus, I didn't actually fix anything and am still getting CTDs occasionally. I did, however, delete a bunch of plugins I rarely use. Log.txt and Log_ATC.txt do not provide a consistent cause of the CTDs. I'm hoping that 12.10 will fix my sim. If not, I'll have to roll-up my sleeves and rebuild everything from scratch.
Thanks for your post. I'm right there with you.