Jonathan White

I can reproduce the "doesn't do anything" aspect.

6 MB? Did you have a huge attachment on an entry?

Technically clearing the recycle bin should wipe out the history since the entry nodes themselves are removed at that point.

I just added a bunch of large attachments and custom icons to entries and deleted them (from the recycle bin) and the size went from 4 MB -> 60 KB....

Show the file properties sheet (from your file manger) for: 

Well that sure is interesting

Do you have anything listed in previous versions? I'm not 100% sure, but that might be counting against your size.

My only thought is entry attachments, there must be one "stuck" somehow to a phantom entry. Attachments are very odd in the kdbx specification and there have been corruption points...

Deleted object lines are fully expected.

9MB of what? That is a LOT of XML. How many entries did you delete, over 1 million?