I did some digging today and found out that only the top level "documents" folder was affected, everything inside it was wiped and replaced by the new stuff I mentioned in my previous post.
All the "extensions" seem to be fine and to get back KUAL I had to run the installation process again, make sure you get the "collate" package if you are running on firmware greater than 5.9 if I recall correctly.
I made the mistake of trying the official non-collate package and it did not work for me.
After doing the install I got back the beloved KUAL booklet in my library, my happiness knew no bounds!
At-least I was able to use this as an excuse to update all of my extensions as well as KOReader
Everything seems to be back to normal now, I restocked my library with my local copies of ebooks, thank god I was not relying solely on my kindle for safe keeping
I hope my experience helps someone out there
Happy reading
