Instead there's an encrypted journal and encrypted data blocks. (Having the additional layer of data blocks allows for better deduplicating one version of a file to the next.) So for each transaction that's uploaded to the servers, we know that the journal gets longer, and that data blocks are added or removed (or both.)
All the database work for keeping track of the data blocks (reference accounting, garbage collection) is done client side. More details in this post from 2009: https://spideroak.com/articles/why--how-spideroak-architectu...