I got the 'root object missing or invalid' error after decrypting one of my books. The resulting file, in other words, is corrupted. Other books came out fine, but this one, it seemed, was lost in the shackles of that stupid Digital Editions contraption that doesn't allow me to read books I've paid for the way I want to.
Luckily, after some experimenting, I've found a solution.
Download and install the demo found here:
http://www.pdf-repair.com/.
Run the program on the corrupted .pdf file (not the original ebook but the decrypted one). You will be shown a preview of the result, but since it's a demo, you can't save the fixed file.
Now open an explorer window and go to C:\Users\<yourname>\AppData\Local\Temp\
Search for a pdf file that was created today; in my case, it was called 'TMPFF0C.pdf'. This is the fixed file.