So, is the title of the thread still accurate? "Missing covers, missing content. Getting worse with each sync."
Did you contact customer support along the line and tell them you were adding .odt files and deleting sql lite files? What was their advice?
Is there some reason you avoid using the tools that come with, and are recommended for use with, the Kobo reader?
I use the Kobo desktop software for anything I acquire from Kobo; and ADE for anything I acquire from the public library or from my own ePubs at Calibre. At no point do I fool around with the internals of Kobo reader and I've had no troubles at all syncing, reading, adding, deleting ... using the Kobo tools.
Yes, I have the sporadic ePub problem with non-Kobo acquired books. Until Kobo fixes that issue, I just read something else.