I noticed this writing unit tests for new WebsiteData API in the GTK+ port. When DatabaseTracker::deleteDatabasesModifiedSince() is called with a min time, all databases for every origin are deleted. For each origin if all databases are removed DatabaseTracker::deleteOrigin() is called to remove also the origin database file. However, DatabaseTracker::deleteOrigin() returns early if the origin doesn't have databases and in this particular case it never has databases, because we have just removed them.
Created attachment 299428 [details] Patch
Committed r211035: <http://trac.webkit.org/changeset/211035>