You could certainly do that, but you'll want to be careful as
you do--there are HTML files in the WebHelp folder that refer to
those JS files, too. That means you'd either have to move all of
those into the scripts folder or amend all of the <script>
tags in those files so they point to the right location.
If you move all of those files into the scripts folder,
you'll have to check the start page (I think the same as what you
called the launch page) for any references to those files so you
can update the paths. Depending on how many there are and whether
the start page changes each time you generate, you may not have
much trouble.
After you move things and verify that the help isn't broken,
you may want to consider using the publish feature to publish to a
second location on your hard drive after you generate. This would
help ensure that the changes you've hard-coded into your files
aren't overwritten in that second location every time you generate.
Then you use the files in the second location to launch your help
to the users.
So the basic answer to your question is yes, but you will
probably have to do some experimenting first to make sure all
references are correct.
If I understand what you're saying, though, you're talking
about putting a scripts folder within the WebHelp folder? In that
case, wouldn't the reference be src="scripts/whver.js"? Or is your
start page not directly within the WebHelp folder?
--Ben