There is a umbraco 4.5 publish bug you may/may not be aware of.
I spent ages trying to figure out why 1 node still appears in the
XML, altough I can't see it in the admin panel.
Basically when you click on the node, on the right - you'll get
the properties panel of the node you've selected. If you remove the
node currently being selected, the properties panel still stays in
place and you're obviously still able to hit save. Once you've
saved it, the node gets published, however it no longer appears in
The easiest solution would be to disable the right properties
panel as soon as you hit delete.
Having done some funther research on umbraco.org, the temp fix
is to remove umbraco.config file and republish the entire site.