Yes me too!!! The opposite way around though, I think.
I installed Calibre fixed the meta data of my PDF books, even adding bookcovers. This took several hours and looked GREAT and worked just like iTunes. I loaded onto my reader and was amazed..... it even put my books into collections. But was I satisfied? Oh no. I just HAD to go over to the Sony bookstore to get my 100 free books, just because I'm not a USA resident and wanted to see if it could be done. Even though I was advised not to bother and knew I could get them anywhere, I still did.
Breezed through registering my account and reader etc. but then the rest took forever, I finally did manage to download some of the free books although navigation on the Sony connect site is dismal, and downloads stopped twice.
Finally finished and very pleased with myself I disconnected only to find that my previously Calibre loaded books were all messed up. The old incorrect meta data once more displayed.

So I deleted the books, leaving only the Sony books. Re-added them again, and still the same.
What do I do?? How can I fix this problem? Is there anyway around this, does anyone know? I don't mind deleting the Sony books

and software and sticking with Calibre, if that will fix the problem.