When you hotsync a HandStory anything to your MS, it goes into the \launcher folder. When you open HandStory and do an "update list" command (or if you have it set to do this automatically), HandStory will move this file from \launcher to \programs\handstory. In this process, the file in \launcher is deleted. That's how it's supposed to work! I just experimented with 1 ebook clip, 1 web clip, and 1 save-to-palm clip, and the above procedure is what happened. (I knew it was working that way, but wanted to run a fresh test before writing this response.)
If you saying that after you create and sync a web clip, and open HandStory and do an update, then via FileZ or MSGate or whatever file utility you have, verify that the same file (size/date) is in both places...then there is something weird happening!
The above behavior began with version 2.0. There is no situation where HandStory would leave a copy in \launcher after moving the file to \programs\handstory, which is does before the file can be read.
If you have v2.0 or greater, and you're still experience identically copies in both places after sync and HS update, then I'd suggesting contacting handstory since you may have some sort of conflict going on within your PDA. There's no reason or condition that I know of where this would happen!
Let us know what you find out if you contact HS.