Each content-type handles delete it’s own way. Documents for example use the Version State. Discussions I believe are either there or not in terms of deletion, but they do have different states for moderation that control their visibility. Blog posts are similar to discussions, except they have the concept of existing prior to being visible as well.
Does that help?
I found out why I was having a problem. The document and Space I was looking at is somehow bugged so a document thought it existed in the space but the space said it didn't have any docs in it. Instead the db was referencing a draft version of the Document as it's current version which was not making it very happy.
For further reference, for documents, it is the "state" column in the jivedocversion table. You will also need the current version found in the jivedocument table to reference the correct information.