Orphaned comments.

One of the possible sources of inconsistency I discovered is that Node Comments doesn't have hook_user() implementation thus it doesn't update own table with when user is deleted.

See #1175348: Node Comments doesn't react on user delete events

Hm, user delete stuff doesn't affect number of rows.
Is it for freshly installed module or did you have previous versions installed ? I can't say anything about previous ones. This module has a very long history, and lots of bugs fixed in the process.

In 3.x I removed comment conversion completely. So we may need to deal with orphans somehow.

One more source of DB inconsistency: node comments were deleted via node_delete() which checks delete permissions. That means user deleting own comments most likely didn't fully delete children comments because of lack of the permission. Need to decide what to do with these nodes.

2.x was such a shame...it was full of bugs and poor architecture.
Ok, the module now deletes "node_comments" table entries one by one, only together with the node. This itself should increase durability: in case mass delete fails, you only get max 1 broken node/comment.

Another thing I implemented is a custom delete function. It doesn't check for delete permissions so when user deletes his own comments, child comments are properly deleted (same way core comment module does). It also allows to veto deletion via custom hook, and also to prepare for delete operation via another hook, if nodeapi "delete" operation is too late. In terms of this issue we only care that it doesn't leave orphans.

We have better db durability now...hopefully