I had a problem syncing about a month ago, although not the exact same as what you've experienced.
I wrote into Kobo and they had me try a bunch of things, and nothing worked until the person who helped me deleted everything from my online library and re-added it. She had me sync then, and it worked. The only thing that bugged me was that she only re-added purchased books, not the free ones I had downloaded, and since there is no record of the free books, she could only help me with the ones I could remember having.
It took about a month from opening the ticket to finally being able to sync properly, but everything's working fine again for me. You should write to Kobo and I'm sure they'll help figure out what's happening, I'm pretty sure your device isn't bricked.