I was having a similar problem with i
CONharvester creating phantom custom themes that could not be deleted. These were based on already installed winterboard themes that IH could not uninstall.
Even when I deleted the original winterboard theme I still had the "... - customized" theme showing up in winterboard.
This page lead me to the solution, in a weird way:
http://iconharvester.com/repairing-permissions - ah, the location of the iconharvester generated icons! Yes, it looks like IconHarvester is using summerboard not winterboard for its themes. Not sure why, I am new to all of this.
Using ssh or whatever (even the current version of iPhone Explorer will suffice), you can cd /var/mobile/Library/SummerBoard/Themes
You should find folders for the unpacked themes in that folder you were talking about.
Delete these folders and files - you may need to delete them individually or recursively if you're using terminal.
If necessary, use Cydia to update to IconHarvester 2.0.1 You should be able to start over at that point.
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Another problem people might find is that in iOS 4.2.1 the camera and photos icons are acting kinda crazy.
Inside IconHarvester's preview, they often both default to the sunflower icon.
Some research lead to me finding that names for both the "Photos" and "Camera" apps having changed.
via:
http://www.pixeldelirious.com/design-tuts/iphone-gui/iphone-theme-changes-required-for-ios-4-2-1/
So I tried a rename...
com.apple.mobileslideshow-Camera.png -> com.apple.camera-Icon.png
com.apple.mobileslideshow-Photos.png -> com.apple.mobileslideshow-Icon.png
But this did not work. Maybe I did the names wrong. Tried a few different things but eventually gave up for now.
Considering the amount of work this involved, I guess one could just as easily make their own Winterboard theme and stay away from IconHarvester until the next update. Unfortunately for those who dropped 4.99 on this slick interface, they must continue to be at the whim of

's continually revolving icon names and remain stuck with the default camera and photos icons.