I don't "Believe" anything.
I have "suspicions"

based from experience. Some prove false

.
The facts supplied by you:
1)Metadata.db exists
2?)There are: a)no Author folders, or b) Book folders within, or c)formats within those
3)The Gui reflects 2b. This sort of indicates a valid Library action.
Do you have some sort of cloud or mirror configured?
do you have some sort of scheduled script against the Library folder


Do ALL these books have a tag
News