I've had that problem for a year now and it's still going on. We're on our 3rd host in that amount of time. I have a thread here from last year: http://www.zen-cart.com/forum/showthread.php?t=91892

I tested deleting a category on someone else's zen install and it was fine. As far as I can tell it's just us. New sites, old sites, different hosts.

I'm just used to having to re-upload when I delete categories. We use a main image directory and then have subaccounts share the files. Even deleting a category in a sub website whose images folder is "virtual" deletes the image from the main site.

I just did it again: othersite.com is a subdir on the server under mainsite.com. Both have zen installs. I deleted a category in othersite.com and the images are now gone from mainsite.com/images. ALL of the subdomains are missing the images, and browsing to mainsite.com/images/image.jpg will show nothing. The files are gone